2025-06-27 22:57
ftp://ftp.de.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=python  --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 -j6
platform: Linux-6.1.0-37-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.67
compiler: g++ (Debian 12.2.0-14+deb12u1) 12.2.0
cppcheck: head 2.17.0
head-info: b6dd286 (2025-06-27 13:53:34 +0200)
count: 3776 3792
elapsed-time: 287.4 302.0
head-timing-info:

old-timing-info:

head results:
hisat2-2.2.1/assert_helpers.h:251:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/assert_helpers.h:269:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/tinythread.h:261:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/tinythread.h:637:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable N [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:87:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:118:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:183:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:191:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:246:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:254:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1075:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1084:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1104:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1119:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1144:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1204:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1212:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1220:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1233:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1241:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1284:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1314:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1351:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1374:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1415:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1424:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1444:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1459:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1482:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1540:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1548:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1569:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1577:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1620:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1650:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1687:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1710:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1753:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1765:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1778:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1800:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1807:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1911:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1919:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1956:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1983:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2027:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2070:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2087:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2131:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2140:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2175:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2200:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2260:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2268:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2276:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2345:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2375:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2409:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2432:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2477:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2559:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2578:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2602:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2642:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2667:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2686:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2728:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2745:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2978:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2986:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3076:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3170:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3210:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3227:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3250:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3268:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3294:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3303:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3317:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3339:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3350:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3384:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3445:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3465:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3474:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3483:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3492:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3516:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3577:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3597:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3606:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3615:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3624:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3648:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3889:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3926:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3980:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4000:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4205:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4350:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4361:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4379:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alphabet.h:149:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alphabet.h:191:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:119:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:256:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:327:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:372:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:398:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:443:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:469:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:626:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:642:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:653:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:661:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:669:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:677:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:688:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:699:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:802:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:816:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:857:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1072:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1089:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1107:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1145:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1153:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1466:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1496:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1543:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1568:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2206:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2221:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2263:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2277:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2285:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2305:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2320:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2332:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2396:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2421:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2434:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2451:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2473:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2526:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2625:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2638:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2653:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2672:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2688:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2703:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2733:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2743:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2753:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2762:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2771:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2787:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2804:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2823:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3198:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3213:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3230:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3249:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3265:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3288:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3297:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3308:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3317:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3350:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3359:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3375:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3394:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3416:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:92:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:164:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:183:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:283:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:315:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:465:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:476:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:505:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:536:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:552:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:561:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:576:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:604:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:627:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:648:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:672:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/filebuf.h:687:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/util.h:34:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:230:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:287:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:299:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:308:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:320:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read.h:410:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alignment [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/tokenize.h:43:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:114:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:346:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:399:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:485:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:773:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:886:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:934:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:950:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_cache.h:987:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2918:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2931:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2946:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2984:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2999:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3013:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3042:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3051:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3062:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3071:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3082:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3097:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3113:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:3132:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1733:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1749:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1775:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1790:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1806:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1818:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1826:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1834:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1934:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1972:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1989:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2051:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2067:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:332:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:341:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:360:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:372:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:398:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:411:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:508:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:528:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:601:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:612:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:628:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:642:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:671:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:709:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:717:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:727:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:782:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:790:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:828:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:837:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:873:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:898:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:918:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:944:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:968:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:1029:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:4101:11: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4123:13: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4149:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4150:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4162:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4163:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4169:10: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/alphabet.h:150:16: warning: Either the condition '(c)<=4' is redundant or the array 'dnacomp[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/alphabet.h:149:2: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/alphabet.h:150:16: note: Array index out of bounds
hisat2-2.2.1/tinythread.h:704:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
hisat2-2.2.1/filebuf.h:351:18: 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]
hisat2-2.2.1/filebuf.h:353:21: note: Assuming that condition 'c==-1' is not redundant
hisat2-2.2.1/filebuf.h:351:18: note: Invalid argument
hisat2-2.2.1/filebuf.h:390:18: 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]
hisat2-2.2.1/filebuf.h:392:21: note: Assuming that condition 'c==-1' is not redundant
hisat2-2.2.1/filebuf.h:390:18: note: Invalid argument
hisat2-2.2.1/random_source.h:39:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:39:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:41:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:43:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:43:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString::cs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString::printcs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString::len_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:2148:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2160:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2167:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2174:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2246:21: warning: Member variable 'SStringFixed::printcs_' is not assigned a value in 'SStringFixed::operator='. [operatorEqVarError]
hisat2-2.2.1/filebuf.h:59:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:59:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:63:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:63:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:69:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:69:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:75:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:75:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:531:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:546:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:560:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:49:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:49:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:51:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:51:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:434:2: warning: Member variable 'PerReadMetrics::tz_beg' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ds.h:4232:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4232:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:43: performance: Variable 'd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/tinythread.h:539:31: style:inconclusive: Technically the member function 'tthread::thread::native_handle' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:154:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::lock' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:183:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::try_lock' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:237:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::unlock' can be const. [functionConst]
hisat2-2.2.1/ds.h:61:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
hisat2-2.2.1/ds.h:67:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
hisat2-2.2.1/ds.h:72:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
hisat2-2.2.1/ds.h:78:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1563:34: performance:inconclusive: Technically the member function 'ELLList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:2283:24: performance:inconclusive: Technically the member function 'ELSet::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:3147:10: style:inconclusive: Technically the member function 'Pool::full' can be const. [functionConst]
hisat2-2.2.1/ds.h:3160:7: performance:inconclusive: Technically the member function 'Pool::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sstring.h:733:7: style:inconclusive: Technically the member function 'SString::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:740:7: style:inconclusive: Technically the member function 'SString::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:747:7: style:inconclusive: Technically the member function 'SString::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:754:7: style:inconclusive: Technically the member function 'SString::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:761:7: style:inconclusive: Technically the member function 'SString::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:768:7: style:inconclusive: Technically the member function 'SString::operator>=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1396:7: style:inconclusive: Technically the member function 'S2bDnaString::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1403:7: style:inconclusive: Technically the member function 'S2bDnaString::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1410:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1417:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1424:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1431:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2342:7: style:inconclusive: Technically the member function 'SStringFixed::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2349:7: style:inconclusive: Technically the member function 'SStringFixed::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2356:7: style:inconclusive: Technically the member function 'SStringFixed::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2363:7: style:inconclusive: Technically the member function 'SStringFixed::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2370:7: style:inconclusive: Technically the member function 'SStringFixed::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:2377:7: style:inconclusive: Technically the member function 'SStringFixed::operator>=' can be const. [functionConst]
hisat2-2.2.1/filebuf.h:84:7: style:inconclusive: Technically the member function 'FileBuf::isOpen' can be const. [functionConst]
hisat2-2.2.1/filebuf.h:117:7: style:inconclusive: Technically the member function 'FileBuf::eof' can be const. [functionConst]
hisat2-2.2.1/filebuf.h:703:14: style:inconclusive: Technically the member function 'OutFileBuf::name' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:122:7: style:inconclusive: Technically the member function 'QKey::toString' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:290:7: style:inconclusive: Technically the member function 'SAVal::valid' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:898:33: style:inconclusive: Technically the member function 'AlignmentCacheIface::current' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1880:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1887:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1894:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1901:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1908:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1915:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 >::operator>=' can be const. [functionConst]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/fast_mutex.h:118:3: warning: Class 'fast_mutex' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const std::basic_string<T>&str)' at line 541. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:541:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const T*b,long sz)' at line 552. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:552:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const T*b)' at line 563. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:563:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const std::basic_string<T>&str)' at line 2161. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2161:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b,long sz)' at line 2168. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2168:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b)' at line 2175. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2175:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2702:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2608. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2608:5: note: Calling installColors
hisat2-2.2.1/sstring.h:2702:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2687:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2610. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2610:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2687:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2671:15: style: Virtual function 'install' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2613. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2613:4: note: Calling install
hisat2-2.2.1/sstring.h:2671:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3264:15: style: Virtual function 'installChars' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3184. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:3184:4: note: Calling installChars
hisat2-2.2.1/sstring.h:3264:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3248:15: style: Virtual function 'install' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3186. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:3186:4: note: Calling install
hisat2-2.2.1/sstring.h:3248:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3034:15: 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 2868. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2868:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3034:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:3026:15: 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 2870. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2870:5: note: Calling installChars
hisat2-2.2.1/sstring.h:3026:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3012:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2889. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2889:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3012:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2998:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2891. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2891:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2998:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2983:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2894. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2894:4: note: Calling install
hisat2-2.2.1/sstring.h:2983:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,bool chars=false,bool colors=false)' at line 2907. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2907:3: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const std::basic_string<char>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const char*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const char*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2732:7: warning: The class 'SDnaStringFixed' defines member function with name 'set' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:2276:7: note: Parent function 'SStringFixed::set'
hisat2-2.2.1/sstring.h:2732:7: note: Derived function 'SDnaStringFixed::set'
hisat2-2.2.1/sstring.h:2779:14: warning: The class 'SDnaStringFixed' defines member function with name 'operator[]' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:2183:18: note: Parent function 'SStringFixed::operator[]'
hisat2-2.2.1/sstring.h:2779:14: note: Derived function 'SDnaStringFixed::operator[]'
hisat2-2.2.1/sstring.h:2786:14: warning: The class 'SDnaStringFixed' defines member function with name 'get' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:2197:18: note: Parent function 'SStringFixed::get'
hisat2-2.2.1/sstring.h:2786:14: note: Derived function 'SDnaStringFixed::get'
hisat2-2.2.1/sstring.h:3041:7: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'set' also defined in its parent class 'SStringExpandable < char , 1024 , 2 >'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1789:7: note: Parent function 'SStringExpandable < char , 1024 , 2 >::set'
hisat2-2.2.1/sstring.h:3041:7: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::set'
hisat2-2.2.1/sstring.h:3050:7: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'append' also defined in its parent class 'SStringExpandable < char , 1024 , 2 >'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1797:7: note: Parent function 'SStringExpandable < char , 1024 , 2 >::append'
hisat2-2.2.1/sstring.h:3050:7: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::append'
hisat2-2.2.1/sstring.h:3089:21: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable < char , 1024 , 2 >'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1817:11: note: Parent function 'SStringExpandable < char , 1024 , 2 >::operator[]'
hisat2-2.2.1/sstring.h:3089:21: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::operator[]'
hisat2-2.2.1/sstring.h:3096:21: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'get' also defined in its parent class 'SStringExpandable < char , 1024 , 2 >'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1833:11: note: Parent function 'SStringExpandable < char , 1024 , 2 >::get'
hisat2-2.2.1/sstring.h:3096:21: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::get'
hisat2-2.2.1/assert_helpers.h:33:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/tinythread.h:579:5: style: Class 'id' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/threading.h:39:5: style: Class 'ThreadSafe' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/random_source.h:41:2: style: Class 'RandomSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2471:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:63:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:69:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:75:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:461:2: style: Class 'BitpairOutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:531:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:546:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:1661:2: style: Class 'SStringExpandable < char , 1024 , 2 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:2617:11: style: The destructor '~SDnaStringFixed' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:2178:11: note: Virtual destructor in base class
hisat2-2.2.1/sstring.h:2617:11: note: Destructor in derived class
hisat2-2.2.1/sstring.h:2910:11: style: The destructor '~SDnaStringExpandable < 1024 , 2 >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:1710:11: note: Virtual destructor in base class
hisat2-2.2.1/sstring.h:2910:11: note: Destructor in derived class
hisat2-2.2.1/sstring.h:2983:15: style: The function 'install' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:1841:15: note: Virtual function in base class
hisat2-2.2.1/sstring.h:2983:15: note: Function in derived class
hisat2-2.2.1/sstring.h:3145:22: style: The function 'toZBuf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:2062:19: note: Virtual function in base class
hisat2-2.2.1/sstring.h:3145:22: note: Function in derived class
hisat2-2.2.1/filebuf.h:567:18: error: Exception thrown in function declared not to throw exceptions. [throwInNoexceptFunction]
hisat2-2.2.1/filebuf.h:513:11: style: Class 'BitpairOutFileBuf' is unsafe, 'BitpairOutFileBuf::out_' can leak by wrong usage. [unsafeClassCanLeak]
hisat2-2.2.1/sstring.h:88:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:193:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:196:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:484:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:504:15: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:686:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/ds.h:3406:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/ds.h:4176:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/read.h:211:9: style: The scope of the variable 'started' can be reduced. [variableScope]
hisat2-2.2.1/read.h:235:9: style: The scope of the variable 'started' can be reduced. [variableScope]
hisat2-2.2.1/ds.h:612:3: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/sstring.h:3419:46: warning: Either the condition '(poss)>(0)' is redundant or there is division by zero at line 3419. [zerodivcond]
hisat2-2.2.1/sstring.h:3418:3: note: Assuming that condition '(poss)>(0)' is not redundant
hisat2-2.2.1/sstring.h:3419:46: note: Division by zero
hisat2-2.2.1/filebuf.h:478:21: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
hisat2-2.2.1/ds.h:3249:14: style: Local variable 'i' shadows outer argument [shadowArgument]
hisat2-2.2.1/ds.h:3245:10: note: Shadowed declaration
hisat2-2.2.1/ds.h:3249:14: note: Shadow variable
hisat2-2.2.1/aligner_cache.h:729:18: style: Parameter 'qv' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_cache.h:773:18: style: Variable 'qv' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/ds.h:3730:34: style: Parameter 'ol' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/sstring.h:786:30: style: Parameter 'rcmap' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/gfm.h:657:9: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/qual.h:47:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/qual.h:109:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/qual.h:167:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/qual.h:198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/qual.h:227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:304:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:313:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:333:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:360:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:371:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:382:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed_policy.cpp:41:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed_policy.cpp:333:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:118:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/endian_swap.h:77:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:116:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:166:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:216:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:266:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:314:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:331:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2412:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:2435:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.h:82:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.h:177:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sequence_io.h:45:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sequence_io.h:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/timer.h:60:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/timer.h:83:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.h:133:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_coord.h:249:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_coord.h:414:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:32:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:59:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:65:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:70:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bitpack.h:76:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:48:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:106:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:124:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:267:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:306:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:324:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:350:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:412:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:493:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:534:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:663:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:687:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:718:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:783:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:815:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:905:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:1053:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/multikey_qsort.h:1150:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:85:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:125:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:168:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:286:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:325:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:388:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:412:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:424:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:703:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/binary_sa_search.h:56:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/zbox.h:41:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:474:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:726:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:788:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:66:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:122:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:189:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:214:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:245:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:285:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:441:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:468:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:518:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_kmer.h:555:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/radix_sort.h:101:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:315:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4352:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4437:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4475:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4521:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4572:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4716:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _gh [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5155:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _gh [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5496:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6464:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6549:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.h:160:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:136:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:174:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:236:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:256:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:307:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:466:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:485:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:834:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1081:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1298:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1383:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1394:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1521:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1530:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1541:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1550:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1560:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1569:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1579:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1602:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1637:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1702:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.h:1881:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:115:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:238:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:249:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:276:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:315:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:405:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:492:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:679:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:779:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:828:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:879:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:904:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:1031:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:1068:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:1120:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_result.cpp:1192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:711:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:1013:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:1187:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:1275:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:1332:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2405:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2432:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2433:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2434:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2509:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2576:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2625:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2683:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2704:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2726:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2747:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2791:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2807:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT2_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2857:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:2964:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3019:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3105:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3152:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3463:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3511:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3553:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3648:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3690:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3718:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3745:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3767:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3856:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3904:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3938:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3965:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4061:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4119:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4177:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4220:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4330:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4718:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5158:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5555:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5616:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5660:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5684:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5729:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5777:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5841:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6566:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6645:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6696:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6751:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6794:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6835:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6903:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6950:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:384:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:436:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:482:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:230:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:245:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1615:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1642:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1718:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1733:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1826:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1871:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1902:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1920:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1962:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2023:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2051:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2088:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sub_temp_nodes [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2172:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2278:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2300:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2318:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2345:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2384:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2785:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:149:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:171:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:215:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:273:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:287:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:333:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:349:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:374:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:817:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:883:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1281:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1313:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/radix_sort.h:203:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:212:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable repID [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:254:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:280:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable repID [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:367:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:389:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:449:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:519:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:151:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable joinedOff [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat.h:170:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tid [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alt.h:242:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alt.h:179:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alt.h:200:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:250:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:278:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:379:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:442:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:543:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:747:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:820:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:923:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:100:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:459:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:520:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:562:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:603:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:726:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:897:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:908:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:927:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:970:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:384:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/blockwise_sa.h:520:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.h:305:26: warning: Either the condition '(q)>=0' is redundant or the array 'mmpens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:304:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:305:26: note: Negative array index
hisat2-2.2.1/scoring.h:334:43: warning: Either the condition '(q)>=0' is redundant or the array 'matchBonuses[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:333:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:334:43: note: Negative array index
hisat2-2.2.1/scoring.h:361:25: warning: Either the condition '(q)>=0' is redundant or the array 'npens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:360:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:361:25: note: Negative array index
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::matchBonuses' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::mmpens' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::npens' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:170:3: performance: Variable 'scoreMin' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/scoring.h:171:3: performance: Variable 'nCeil' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < string , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < string , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < string , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/qual.h:117:10: style: Condition 'cc<33' is always false [knownConditionTrueFalse]
hisat2-2.2.1/qual.h:116:40: note: Assignment 'cc=solexaToPhred((int)c-64)+33', assigned value is greater than 32
hisat2-2.2.1/qual.h:117:10: note: Condition 'cc<33' is always false
hisat2-2.2.1/scoring.h:181:28: style: Condition 'matchType==COST_MODEL_CONSTANT' is always true [knownConditionTrueFalse]
hisat2-2.2.1/scoring.h:163:18: note: Assignment 'matchType=COST_MODEL_CONSTANT', assigned value is 3
hisat2-2.2.1/scoring.h:181:28: note: Condition 'matchType==COST_MODEL_CONSTANT' is always true
hisat2-2.2.1/aligner_seed.h:162:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:175:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:191:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:204:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:655:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:688:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:913:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:922:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:949:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1009:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1052:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1096:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1119:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1128:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1168:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1651:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1768:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1860:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1892:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:2033:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:2392:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:2467:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:2611:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:2668:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.cpp:105:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/dp_framer.h:103:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:38:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:106:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:152:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:222:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:304:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:358:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:434:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:449:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sse_util.h:471:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:256:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:408:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:462:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:478:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:488:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:556:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_st_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.h:638:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/mask.h:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:53:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:603:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:1157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:1246:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:1361:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:1474:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/random_util.h:130:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:123:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:410:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:419:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:427:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:481:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:521:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:899:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:920:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:931:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:952:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:967:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:978:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:1016:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:1050:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:1481:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:1504:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/group_walk.h:1561:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:319:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:542:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:658:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:907:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1189:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1237:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1384:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1456:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1594:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1635:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1648:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1741:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1782:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1794:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1953:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:1976:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2153:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable botf [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2193:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2415:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2537:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2630:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pen [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2713:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2827:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapadd_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:2925:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off5p [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3027:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3376:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3483:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3563:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3748:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed2.h:3828:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/unique.h:64:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/unique.h:123:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/unique.h:197:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/unique.h:455:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sam.h:170:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sam.h:579:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable snpID [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:286:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:316:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:576:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:601:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:777:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1164:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1367:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1395:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1571:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spliceSiteDB_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1620:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1651:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:1998:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:2690:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:2780:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.h:3237:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable altdb_ [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alt.h:180:13: warning: Comparison of a boolean expression with an integer. [compareBoolExpressionWithInt]
hisat2-2.2.1/aligner_result.h:249:29: style:inconclusive: Boolean expression 'repeat_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/aligner_result.h:252:49: style:inconclusive: Boolean expression 'knownTranscripts_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/aligner_result.h:253:47: style:inconclusive: Boolean expression 'nearSpliceSites_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/multikey_qsort.h:1083:21: warning: Either the condition '(c)<=4' is redundant or the array 'bkts[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/multikey_qsort.h:1079:13: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/multikey_qsort.h:1083:21: note: Array index out of bounds
hisat2-2.2.1/multikey_qsort.h:1083:31: warning: Either the condition '(c)<=4' is redundant or the array 'cnts[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/multikey_qsort.h:1079:13: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/multikey_qsort.h:1083:31: note: Array index out of bounds
hisat2-2.2.1/timer.h:75:12: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
hisat2-2.2.1/ref_read.h:229:3: 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]
hisat2-2.2.1/ref_read.h:182:2: note: Assuming that condition '-1!=(lastc)' is not redundant
hisat2-2.2.1/ref_read.h:194:4: note: c is assigned 'lastc' here.
hisat2-2.2.1/ref_read.h:229:3: note: Invalid argument
hisat2-2.2.1/ds.h:529:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
hisat2-2.2.1/ds.h:536:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
hisat2-2.2.1/aligner_result.h:902:2: warning: Member variable 'AlnRes::repeat_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_result.h:914:5: warning:inconclusive: Member variable 'AlnRes::drd' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
hisat2-2.2.1/aligner_result.h:914:5: warning: Member variable 'AlnRes::seedival_' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_result.h:966:13: warning:inconclusive: Member variable 'AlnRes::drd' is not assigned a value in 'AlnRes::operator='. [operatorEqVarError]
hisat2-2.2.1/aligner_result.h:966:13: warning: Member variable 'AlnRes::seedival_' is not assigned a value in 'AlnRes::operator='. [operatorEqVarError]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < uint32_t >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offMask' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offsLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offsSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_lineSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideGbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideGbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numSides' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numLines' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtTotLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtTotSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numNodes' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:100:9: warning:inconclusive: Member variable 'Edge::from' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:100:9: warning:inconclusive: Member variable 'Edge::to' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:305:9: warning: Member variable 'CompositeNode::value' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::tid' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::toff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::joinedOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:50:5: warning: Member variable 'RepeatCoord < uint32_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint32_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint32_t >::reversed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ls.h:43:1: style: The class 'LarssonSadakane < int >' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString < char >::cs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString < char >::printcs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:584:14: warning: Member variable 'SString < char >::len_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange'
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange'
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint32_t >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint32_t >::get_alt_range'
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint32_t >::get_alt_range'
hisat2-2.2.1/ref_read.h:48:3: performance: Variable 'msg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:925:9: performance: Variable 'score_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:926:9: performance: Variable 'oscore_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:927:9: performance: Variable 'refcoord_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:929:9: performance: Variable 'refival_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/timer.h:50:7: style:inconclusive: Technically the member function 'Timer::write' can be const. [functionConst]
hisat2-2.2.1/repeat_kmer.h:170:10: style:inconclusive: Technically the member function 'RB_Alignment_CMPbyLen::operator()' can be const. [functionConst]
hisat2-2.2.1/gbwt_graph.h:43:17: performance:inconclusive: Either there is a missing 'override', or the member function 'NongraphException::what' can be static. [functionStatic]
hisat2-2.2.1/gbwt_graph.h:51:17: performance:inconclusive: Either there is a missing 'override', or the member function 'ExplosionException::what' can be static. [functionStatic]
hisat2-2.2.1/splice_site.h:544:10: style:inconclusive: Technically the member function 'SpliceSiteDB::empty' can be const. [functionConst]
hisat2-2.2.1/aligner_result.cpp:1043:14: performance:inconclusive: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_result.h:1357:8: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_result.cpp:1043:14: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < uint32_t >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < uint32_t >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < uint32_t >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < uint32_t >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < uint32_t >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < uint32_t >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < uint32_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < uint32_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/diff_sample.h:509:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < S2bDnaString >::print' can be const. [functionConst]
hisat2-2.2.1/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane < int >::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sstring.h:1880:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1887:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1894:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1901:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1908:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1915:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 >::operator>=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:733:7: style:inconclusive: Technically the member function 'SString < char >::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:740:7: style:inconclusive: Technically the member function 'SString < char >::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:747:7: style:inconclusive: Technically the member function 'SString < char >::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:754:7: style:inconclusive: Technically the member function 'SString < char >::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:761:7: style:inconclusive: Technically the member function 'SString < char >::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:768:7: style:inconclusive: Technically the member function 'SString < char >::operator>=' can be const. [functionConst]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < SpliceSite , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < Pool * , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < RefRecord , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < RefRecord , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < RefRecord , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint8_t , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint8_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint8_t , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SString < char > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SString < char > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SString < char > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint32_t , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint32_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint32_t , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < unsigned long , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < unsigned long , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < unsigned long , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < uint64_t , uint32_t > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < uint64_t , uint32_t > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < uint64_t , uint32_t > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SpliceSite , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SpliceSite , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SpliceSite , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < ALT < uint32_t > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < ALT < uint32_t > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < ALT < uint32_t > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < RedBlack < SpliceSitePos , uint32_t > * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < RedBlack < SpliceSitePos , uint32_t > * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < RedBlack < SpliceSitePos , uint32_t > * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < tthread :: fast_mutex , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < tthread :: fast_mutex , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < tthread :: fast_mutex , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Exon , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Exon , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Exon , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Edit , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Edit , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Edit , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < char , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < char , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < char , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < bool , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < bool , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < bool , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < ESet < RedundantCell > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < ESet < RedundantCell > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < ESet < RedundantCell > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < AlnRes , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < AlnRes , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < AlnRes , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < tthread :: thread * >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < tthread :: thread * >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/splice_site.h:185:15: style: Virtual function 'reset' is called from constructor 'SpliceSitePos()' at line 87. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/splice_site.h:87:20: note: Calling reset
hisat2-2.2.1/splice_site.h:185:15: note: reset is a virtual function
hisat2-2.2.1/splice_site.h:322:15: style: Virtual function 'reset' is called from constructor 'SpliceSite()' at line 256. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/splice_site.h:256:17: note: Calling reset
hisat2-2.2.1/splice_site.h:322:15: note: reset is a virtual function
hisat2-2.2.1/blockwise_sa.h:352:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < S2bDnaString >(const S2bDnaString&__text,uint32_t __bucketSz,int __nthreads,uint32_t __dcV,uint32_t __seed=0,bool __sanityCheck=false,bool __passMemExc=false,bool __verbose=false,std::string base_fname="",ostream&__logger=cout)' at line 206. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/blockwise_sa.h:206:29: note: Calling reset
hisat2-2.2.1/blockwise_sa.h:352:15: note: reset is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const std::basic_string<std::uint32_t>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const uint32_t*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const uint32_t*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const std::basic_string<char>&str)' at line 541. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:541:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b,long sz)' at line 552. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:552:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b)' at line 563. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:563:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/timer.h:37:2: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/gfm.h:306:2: style: Class 'GFMFileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_result.h:2028:2: style: Class 'RedundantAlns' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/gbwt_graph.h:347:9: style: Struct 'TempNodeLabelCmp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:1661:2: style: Class 'SStringExpandable < uint32_t , 1024 , 2 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < SpliceSitePos , uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < tthread :: thread * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/splice_site.h:322:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/splice_site.h:185:15: note: Virtual function in base class
hisat2-2.2.1/splice_site.h:322:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:208:6: style: The destructor '~KarkkainenBlockwiseSA < S2bDnaString >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:85:11: note: Virtual destructor in base class
hisat2-2.2.1/blockwise_sa.h:208:6: note: Destructor in derived class
hisat2-2.2.1/blockwise_sa.h:269:24: style: The function 'nextSuffix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:90:21: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:269:24: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:331:18: style: The function 'nextBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:146:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:331:18: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:337:15: style: The function 'hasMoreBlocks' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:148:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:337:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:352:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:138:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:352:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:361:15: style: The function 'isReset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:140:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:361:15: note: Function in derived class
hisat2-2.2.1/aligner_result.h:1277:21: performance: Function 'score()' should return member 'score_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:1278:21: performance: Function 'oscore()' should return member 'oscore_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2229:11: performance: Function 'best1()' should return member 'best1_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2230:11: performance: Function 'secbest1()' should return member 'secbest1_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2231:11: performance: Function 'best2()' should return member 'best2_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2232:11: performance: Function 'secbest2()' should return member 'secbest2_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2233:11: performance: Function 'bestPaired()' should return member 'bestPaired_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_result.h:2234:11: performance: Function 'secbestPaired()' should return member 'secbestPaired_' by const reference. [returnByReference]
hisat2-2.2.1/ref_read.h:298:14: style: Expression is always true because 'else if' condition is opposite to previous condition at line 296. [multiCondition]
hisat2-2.2.1/ref_read.h:296:13: note: first condition
hisat2-2.2.1/ref_read.h:298:14: note: else if condition is opposite to first condition
hisat2-2.2.1/gbwt_graph.h:1998:8: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/gbwt_graph.h:1997:8: note: First condition
hisat2-2.2.1/gbwt_graph.h:1998:8: note: Second condition
hisat2-2.2.1/gbwt_graph.h:2617:8: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/gbwt_graph.h:2616:8: note: First condition
hisat2-2.2.1/gbwt_graph.h:2617:8: note: Second condition
hisat2-2.2.1/alt.h:180:13: style: Comparing expression of type 'bool' against value 1. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/diff_sample.h:228:13: style: Condition 'keepGoing' is always false [knownConditionTrueFalse]
hisat2-2.2.1/diff_sample.h:199:22: note: Assignment 'keepGoing=false', assigned value is 0
hisat2-2.2.1/diff_sample.h:228:13: note: Condition 'keepGoing' is always false
hisat2-2.2.1/aligner_result.h:1613:8: style: Condition 'sameChr' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_result.h:1612:19: note: Assignment 'sameChr=true', assigned value is 1
hisat2-2.2.1/aligner_result.h:1613:8: note: Condition 'sameChr' is always true
hisat2-2.2.1/gfm.h:2974:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:2973:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:2969:83: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:2974:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3034:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3033:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3029:73: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3034:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3113:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3112:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3108:73: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3113:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3214:12: style: Condition '!usePOPCNT' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3170:26: note: Assignment 'usePOPCNT=false', assigned value is 0
hisat2-2.2.1/gfm.h:3214:12: note: Condition '!usePOPCNT' is always true
hisat2-2.2.1/gfm.h:3436:12: style: Condition '!usePOPCNT' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3388:26: note: Assignment 'usePOPCNT=false', assigned value is 0
hisat2-2.2.1/gfm.h:3436:12: note: Condition '!usePOPCNT' is always true
hisat2-2.2.1/gfm.h:6263:20: style: Condition 'loadFtab' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:6241:12: note: Assuming that condition 'loadFtab' is not redundant
hisat2-2.2.1/gfm.h:6263:20: note: Condition 'loadFtab' is always true
hisat2-2.2.1/gfm.h:6938:16: style: Condition 'mirror' is always false [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:6929:8: note: Assuming that condition 'mirror' is not redundant
hisat2-2.2.1/gfm.h:6938:16: note: Condition 'mirror' is always false
hisat2-2.2.1/util.h:46:27: style: Condition 'value!=0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/util.h:46:13: note: Assuming that condition 'value<=0' is not redundant
hisat2-2.2.1/util.h:46:27: note: Condition 'value!=0' is always false
hisat2-2.2.1/gfm.h:4595:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4757:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4779:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5076:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5201:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5221:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5448:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:2217:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:6070:13: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:6848:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:570:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:623:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:957:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:978:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:1022:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:1072:29: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:2807:9: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
hisat2-2.2.1/word_io.h:106:15: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:148:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:198:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:248:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:298:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:313:13: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:331:10: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:688:34: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:64:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:133:84: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4946:15: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4949:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4949:57: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:5381:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:5667:62: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6061:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6119:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6169:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6171:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6254:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6284:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6320:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6379:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6410:40: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6656:20: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2012:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2041:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2093:35: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2095:70: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2137:33: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2139:68: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2310:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2337:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2426:34: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2428:69: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2462:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2464:67: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:500:35: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:502:69: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:867:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:210:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:212:75: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:248:35: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:251:75: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:281:84: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:174:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:160:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:235:52: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:280:78: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:636:44: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:638:80: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:757:37: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:760:42: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:806:83: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:867:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:868:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/word_io.h:374:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:501:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/endian_swap.h:31:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:37:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:45:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:55:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:63:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:73:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:81:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:91:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:99:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:115:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:165:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:215:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:265:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3151:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3210:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3254:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3357:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3432:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3792:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3794:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3813:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3815:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3984:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:3986:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:4058:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:4060:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:4125:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:6387:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:6407:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/blockwise_sa.h:445:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:321:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:1736:46: style: The comparison 'seqlen <= 16' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:1736:42: note: 'seqlen' is assigned value '16' here.
hisat2-2.2.1/gfm.h:1736:46: note: The comparison 'seqlen <= 16' is always true.
hisat2-2.2.1/gfm.h:1768:46: style: The comparison 'seqlen <= 16' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:1768:42: note: 'seqlen' is assigned value '16' here.
hisat2-2.2.1/gfm.h:1768:46: note: The comparison 'seqlen <= 16' is always true.
hisat2-2.2.1/gfm.h:4010:17: style: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:3975:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4010:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:4083:17: style: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:4049:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4083:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:2857:9: style: Statements following 'return' will never be executed. [unreachableCode]
hisat2-2.2.1/gbwt_graph.h:2622:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
hisat2-2.2.1/blockwise_sa.h:471:9: style: The scope of the variable 'len' can be reduced. [variableScope]
hisat2-2.2.1/aligner_result.cpp:1061:31: style: The scope of the variable 'right' can be reduced. [variableScope]
hisat2-2.2.1/aligner_result.cpp:1111:31: style: The scope of the variable 'right' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:2254:7: style: The scope of the variable 'iter' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:2255:8: style: The scope of the variable 'first' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:4816:21: style: The scope of the variable 'pos' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:5556:11: style: The scope of the variable 'fraglen' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:6091:10: style: The scope of the variable 'shmemLeader' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:6935:13: style: The scope of the variable 'lastorig' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:938:16: style: The scope of the variable 'lo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1038:17: style: The scope of the variable 'kHi' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1038:27: style: The scope of the variable 'kLo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1039:17: style: The scope of the variable 'jHi' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1039:27: style: The scope of the variable 'jLo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1040:14: style: The scope of the variable 'kHiSoft' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1040:31: style: The scope of the variable 'kLoSoft' can be reduced. [variableScope]
hisat2-2.2.1/diff_sample.h:742:16: style: The scope of the variable 'nextRank' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:101:8: style: The scope of the variable 'pl' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:101:18: style: The scope of the variable 'pn' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:102:7: style: The scope of the variable 's' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:128:7: style: The scope of the variable 'f' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:189:18: style: The scope of the variable 'd' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:189:21: style: The scope of the variable 'g' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:288:8: style: The scope of the variable 'pi' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:289:10: style: The scope of the variable 'j' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:289:16: style: The scope of the variable 'sl' can be reduced. [variableScope]
hisat2-2.2.1/multikey_qsort.h:932:2: style: Unsigned expression 'lim' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:249:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:250:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:276:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:277:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/gfm.h:6866:9: style: Unsigned expression 'this->plen()[i]' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/diff_sample.h:614:3: style: Unsigned expression 'sz' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/bitpack.h:39:17: error: Shifting by a negative value is undefined behaviour [shiftNegative]
hisat2-2.2.1/aligner_result.cpp:900:8: style:inconclusive: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_result.h:820:37: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:900:8: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:935:46: style:inconclusive: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_result.h:826:35: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:935:46: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/gfm.h:5605:45: style:inconclusive: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2928:47: note: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'.
hisat2-2.2.1/gfm.h:5605:45: note: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'.
hisat2-2.2.1/gfm.h:5748:38: style:inconclusive: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2472:12: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
hisat2-2.2.1/gfm.h:5748:38: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
hisat2-2.2.1/gfm.h:5749:38: style:inconclusive: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2473:12: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
hisat2-2.2.1/gfm.h:5749:38: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:2363:59: style:inconclusive: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1598:43: note: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:2363:59: note: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/diff_sample.h:154:16: style: Local variable 'ds' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:150:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:154:16: note: Shadow variable
hisat2-2.2.1/diff_sample.h:241:8: style: Local variable 'i' shadows outer argument [shadowArgument]
hisat2-2.2.1/diff_sample.h:141:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:241:8: note: Shadow variable
hisat2-2.2.1/diff_sample.h:291:10: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:262:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:291:10: note: Shadow variable
hisat2-2.2.1/diff_sample.h:302:10: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:262:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:302:10: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:88:36: style: Local variable 'minimizer' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_kmer.h:70:32: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:88:36: note: Shadow variable
hisat2-2.2.1/aligner_result.h:325:18: style: Local variable 'score' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:311:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.h:325:18: note: Shadow variable
hisat2-2.2.1/aligner_result.h:339:18: style: Local variable 'splicescore' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:317:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.h:339:18: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:490:7: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1273:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:490:7: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:497:13: style: Local variable 'reflen' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1330:10: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:497:13: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:498:13: style: Local variable 'refoff' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1123:17: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:498:13: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:11: style: Local variable 'best' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2255:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:11: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:20: style: Local variable 'secbest' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2279:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:20: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:32: style: Local variable 'bestPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2233:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:32: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:44: style: Local variable 'secbestPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2234:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:44: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1187:7: style: Local variable 'paired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2237:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1187:7: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:14: style: Local variable 'numAlns1' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2244:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:14: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:28: style: Local variable 'numAlns2' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2245:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:28: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:42: style: Local variable 'numAlnsPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2246:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:42: note: Shadow variable
hisat2-2.2.1/gfm.h:1939:29: style: Local variable 'tmp_len' shadows outer variable [shadowVariable]
hisat2-2.2.1/gfm.h:1365:25: note: Shadowed declaration
hisat2-2.2.1/gfm.h:1939:29: note: Shadow variable
hisat2-2.2.1/gfm.h:2968:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2968:21: note: Shadow variable
hisat2-2.2.1/gfm.h:2972:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2972:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3028:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3028:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3032:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3032:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3107:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3107:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3111:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3111:21: note: Shadow variable
hisat2-2.2.1/gfm.h:4716:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4716:31: note: Shadow variable
hisat2-2.2.1/gfm.h:4736:11: style: Local variable 'fchr' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2437:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4736:11: note: Shadow variable
hisat2-2.2.1/gfm.h:4737:17: style: Local variable 'ftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2438:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4737:17: note: Shadow variable
hisat2-2.2.1/gfm.h:4787:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4787:10: note: Shadow variable
hisat2-2.2.1/gfm.h:5068:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2439:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5068:20: note: Shadow variable
hisat2-2.2.1/gfm.h:5155:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5155:31: note: Shadow variable
hisat2-2.2.1/gfm.h:5178:14: style: Local variable 'fchr' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2437:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5178:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5179:20: style: Local variable 'ftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2438:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5179:20: note: Shadow variable
hisat2-2.2.1/gfm.h:5229:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5229:10: note: Shadow variable
hisat2-2.2.1/gfm.h:5440:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2439:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5440:20: note: Shadow variable
hisat2-2.2.1/gfm.h:6003:25: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6003:25: note: Shadow variable
hisat2-2.2.1/gfm.h:6146:14: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
hisat2-2.2.1/gfm.h:6091:10: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6146:14: note: Shadow variable
hisat2-2.2.1/gfm.h:6206:17: style: Local variable 'zOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2432:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6206:17: note: Shadow variable
hisat2-2.2.1/gfm.h:6407:31: style: Local variable 'offs' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2440:23: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6407:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6608:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6608:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6692:5: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6692:5: note: Shadow variable
hisat2-2.2.1/gfm.h:6791:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6791:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6792:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6792:10: note: Shadow variable
hisat2-2.2.1/gfm.h:6831:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6831:31: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2506:21: style: Local variable 'past_nodes' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:1684:21: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2506:21: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2739:25: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:2712:17: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2739:25: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:639:25: style: Local variable 's' shadows outer argument [shadowArgument]
hisat2-2.2.1/gbwt_graph.h:363:50: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:639:25: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:955:25: style: Local variable 's' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:870:26: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:955:25: note: Shadow variable
hisat2-2.2.1/radix_sort.h:270:13: style: Local variable 'st' shadows outer variable [shadowVariable]
hisat2-2.2.1/radix_sort.h:200:8: note: Shadowed declaration
hisat2-2.2.1/radix_sort.h:270:13: note: Shadow variable
hisat2-2.2.1/repeat.h:284:45: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:284:45: note: Shadow variable
hisat2-2.2.1/repeat.h:335:21: style: Local variable 'r' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat.h:311:24: note: Shadowed declaration
hisat2-2.2.1/repeat.h:335:21: note: Shadow variable
hisat2-2.2.1/repeat.h:364:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:364:47: note: Shadow variable
hisat2-2.2.1/repeat.h:386:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:386:47: note: Shadow variable
hisat2-2.2.1/repeat.h:446:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:446:47: note: Shadow variable
hisat2-2.2.1/repeat.h:518:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:518:47: note: Shadow variable
hisat2-2.2.1/diff_sample.h:560:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:560:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:568:12: style: Local variable 'd' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:491:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:568:12: note: Shadow variable
hisat2-2.2.1/diff_sample.h:599:25: style: Local variable 'ds' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:495:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:599:25: note: Shadow variable
hisat2-2.2.1/diff_sample.h:601:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:601:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:602:11: style: Local variable 'd' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:491:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:602:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:729:14: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:729:14: note: Shadow variable
hisat2-2.2.1/diff_sample.h:963:25: style: Local variable 'dmap' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:496:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:963:25: note: Shadow variable
hisat2-2.2.1/diff_sample.h:969:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:969:11: note: Shadow variable
hisat2-2.2.1/aligner_result.h:1216:25: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2096:12: performance: Function parameter 'best1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2097:12: performance: Function parameter 'secbest1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2098:12: performance: Function parameter 'best2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2099:12: performance: Function parameter 'secbest2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2100:12: performance: Function parameter 'bestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2101:12: performance: Function parameter 'secbestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2170:12: performance: Function parameter 'best1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2171:12: performance: Function parameter 'secbest1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2172:12: performance: Function parameter 'best2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2173:12: performance: Function parameter 'secbest2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2174:12: performance: Function parameter 'bestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2175:12: performance: Function parameter 'secbestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.cpp:140:21: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.cpp:147:21: performance: Function parameter 'refcoord' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat_kmer.h:384:35: style: Variable 'position' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:4592:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:4753:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:4775:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:5072:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:5197:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:5217:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:5444:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_result.cpp:478:12: style: Parameter 'qseq' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gfm.h:3740:61: style: Parameter 'tloc' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gfm.h:3740:87: style: Parameter 'bloc' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gfm.h:6067:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:6160:32: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:6309:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:6349:36: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gfm.h:6846:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gbwt_graph.h:1519:51: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeFrom' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:1970:14: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1519:51: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:1523:50: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeKey' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:2507:104: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1523:50: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:1569:49: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathEdgeTo' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:2610:102: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1569:49: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:2015:25: style: Variable 'graph' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gbwt_graph.h:109:29: style: Parameter 'f_in' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gbwt_graph.h:121:34: style: Parameter 'a' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gbwt_graph.h:1418:28: style: Variable 'predecessor_cnode' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/alt.h:239:25: style: Parameter 'f_in' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/blockwise_sa.h:568:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/blockwise_sa.h:621:32: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/blockwise_sa.h:955:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/blockwise_sa.h:1020:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_result.cpp:567:11: style: Variable 'refbuf' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/aligner_result.cpp:918:6: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/aligner_result.cpp:950:23: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/timer.h:72:13: style: Variable 'current' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/gbwt_graph.h:2014:25: style: Variable 'en' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/multikey_qsort.h:323:53: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/aligner_swsse.h:123:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:135:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:147:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:171:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:183:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:442:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:467:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.h:492:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:84:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:155:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:281:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:482:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.cpp:715:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_nuc.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_nuc.h:246:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:1066:3: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
hisat2-2.2.1/gfm.h:1076:3: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
hisat2-2.2.1/bitpack.h:45:18: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 44. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:44:2: note: Assuming that condition 'off<16' is not redundant
hisat2-2.2.1/bitpack.h:45:18: note: Shift
hisat2-2.2.1/bitpack.h:50:19: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 49. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:49:2: note: Assuming that condition 'off<16' is not redundant
hisat2-2.2.1/bitpack.h:50:19: note: Shift
hisat2-2.2.1/bitpack.h:72:21: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 71. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:71:5: note: Assuming that condition 'off<32' is not redundant
hisat2-2.2.1/bitpack.h:72:21: note: Shift
hisat2-2.2.1/bitpack.h:77:22: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 76. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:76:5: note: Assuming that condition 'off<32' is not redundant
hisat2-2.2.1/bitpack.h:77:22: note: Shift
hisat2-2.2.1/radix_sort.h:193:16: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
hisat2-2.2.1/radix_sort.h:192:33: note: Assignment 'log_size=sizeof(maxv)*8', assigned value is 32
hisat2-2.2.1/radix_sort.h:193:16: note: Shift
hisat2-2.2.1/repeat_kmer.h:218:25: style: Variable 'curr_in' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_kmer.h:219:26: style: Variable 'est_count' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4626:11: style: Unused variable: name [unusedVariable]
hisat2-2.2.1/gfm.h:4622:18: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4656:25: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4657:11: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4669:11: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:6935:22: style: Variable 'lastorig' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:6951:22: style: Variable 'lastorig' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gbwt_graph.h:1945:11: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gbwt_graph.h:2148:11: style: Variable 'indiv' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:2831:9: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
hisat2-2.2.1/ds.h:529:3: portability: Using memset() on class which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/ds.h:536:3: portability: Using memset() on class which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seq' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::qual' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::maxjump' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedoff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedoffidx' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedtypeidx' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::nfiltered' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:616:2: warning: Member variable 'SeedResults::sorted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ebwtFw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ebwtBw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::s_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::read_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::seq_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::qual_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::fw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ca_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:471:7: performance:inconclusive: Technically the member function 'InstantiatedSeed::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed.h:1611:28: performance:inconclusive: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed.h:1407:7: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed.h:1611:28: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Seed , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Seed , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Seed , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < int , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < int , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < int , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < int , int > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < int , int > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < int , int > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed.h:1147:17: performance: Function 'exactFwEEHit()' should return member 'exactFwHit_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_seed.h:1152:17: performance: Function 'exactRcEEHit()' should return member 'exactRcHit_' by const reference. [returnByReference]
hisat2-2.2.1/aligner_seed.h:2332:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2332:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2333:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2333:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2340:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2340:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2341:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2341:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2042:9: style: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_seed.h:2043:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
hisat2-2.2.1/aligner_seed.h:2042:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
hisat2-2.2.1/aligner_seed.h:2866:6: style: Statements following 'throw' will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed.h:2164:9: style: The scope of the variable 'quc' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.h:2794:15: style: The scope of the variable 'insCons' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.cpp:207:15: style: The scope of the variable 'cons' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.cpp:209:7: style: The scope of the variable 'q' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.h:1742:35: style:inconclusive: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:1442:25: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
hisat2-2.2.1/aligner_seed.h:1742:35: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
hisat2-2.2.1/aligner_seed.cpp:50:59: style:inconclusive: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:276:55: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
hisat2-2.2.1/aligner_seed.cpp:50:59: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
hisat2-2.2.1/aligner_seed.cpp:97:20: style:inconclusive: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:381:21: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
hisat2-2.2.1/aligner_seed.cpp:97:20: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
hisat2-2.2.1/aligner_seed.h:544:7: style: Local variable 'ns' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed.h:529:6: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:544:7: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:2477:22: style: Local variable 'tloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed.h:2465:21: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:2477:22: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:2477:28: style: Local variable 'bloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed.h:2465:27: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:2477:28: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:1890:33: style: Parameter 'met' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_seed.h:1621:43: style: Variable 'seedlen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:2259:16: style: Variable 'offstr' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:2825:22: style: Variable 'loff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.cpp:63:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse.cpp:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/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]
hisat2-2.2.1/mask.h:63:2: note: Assuming that condition 'mask<32' is not redundant
hisat2-2.2.1/mask.h:64:31: note: Array index out of bounds
hisat2-2.2.1/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]
hisat2-2.2.1/mask.h:63:2: note: Assuming that condition 'mask<32' is not redundant
hisat2-2.2.1/mask.h:66:2: note: Array index out of bounds
hisat2-2.2.1/aligner_sw_common.h:42:2: warning: Member variable 'SwResult::nup' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw_common.h:42:2: warning: Member variable 'SwResult::ndn' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::refl_pretrim' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::refr_pretrim' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::maxgap' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::sortedSel_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::cur_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmm_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmm_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdop_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfop_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdex_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfex_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmmPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmmPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdopPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfopPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdexPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfexPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::row_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::col_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:112:7: style:inconclusive: Technically the member function 'DPRect::initIval' can be const. [functionConst]
hisat2-2.2.1/dp_framer.h:241:7: performance:inconclusive: Technically the member function 'DynProgFramer::trimToRef' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:2283:24: performance:inconclusive: Technically the member function 'ELSet < unsigned long , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: 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]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < CpQuad , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < CpQuad , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < CpQuad , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < CpQuad , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < std :: pair < int64_t , unsigned long > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: 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]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < std :: pair < int64_t , unsigned long > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/dp_framer.h:61:2: style: Struct 'DPRect' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/dp_framer.h:126:2: style: Class 'DynProgFramer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sse_util.h:386:6: style: Condition 'debug_' is always true [knownConditionTrueFalse]
hisat2-2.2.1/sse_util.h:370:12: note: Assignment 'debug_=true', assigned value is 1
hisat2-2.2.1/sse_util.h:386:6: note: Condition 'debug_' is always true
hisat2-2.2.1/aligner_bt.cpp:1332:7: style: Condition 'prune' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1322:17: note: Assignment 'prune=false', assigned value is 0
hisat2-2.2.1/aligner_bt.cpp:1332:7: note: Condition 'prune' is always false
hisat2-2.2.1/aligner_bt.cpp:1528:17: style: Condition 'hi-lo<hi_sm-lo_sm' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1515:13: note: Assuming that condition 'newhi>newlo' is not redundant
hisat2-2.2.1/aligner_bt.cpp:1527:19: note: lo_sm is assigned 'newlo' here.
hisat2-2.2.1/aligner_bt.cpp:1527:36: note: Assignment 'hi_sm=newhi', assigned value is less than symbolic=lo_sm
hisat2-2.2.1/aligner_bt.cpp:1528:17: note: Condition 'hi-lo<hi_sm-lo_sm' is always false
hisat2-2.2.1/sse_util.h:410:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/sse_util.h:410:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/sse_util.h:487:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/sse_util.h:487:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_bt.cpp:704:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_bt.cpp:705:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_bt.cpp:716:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_bt.cpp:717:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/sse_util.h:417:17: style: Variable 'asc' is assigned an expression that holds the same value. [redundantAssignment]
hisat2-2.2.1/sse_util.h:411:15: note: asc is assigned 'MIN_I64' here.
hisat2-2.2.1/sse_util.h:417:17: note: Variable 'asc' is assigned an expression that holds the same value.
hisat2-2.2.1/sse_util.h:494:17: style: Variable 'asc' is assigned an expression that holds the same value. [redundantAssignment]
hisat2-2.2.1/sse_util.h:488:15: note: asc is assigned 'MIN_I64' here.
hisat2-2.2.1/sse_util.h:494:17: note: Variable 'asc' is assigned an expression that holds the same value.
hisat2-2.2.1/mask.h:76:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/aligner_bt.cpp:647:9: style: The scope of the variable 'xi' can be reduced. [variableScope]
hisat2-2.2.1/aligner_bt.cpp:1170:9: style: The scope of the variable 'iters' can be reduced. [variableScope]
hisat2-2.2.1/aligner_bt.cpp:696:25: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:696:25: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:726:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:726:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:727:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:727:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:755:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:755:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:760:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:760:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:852:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:852:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:853:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:853:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:854:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:854:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/sse_util.h:218:12: style: Local variable 'last_alloc_' shadows outer variable [shadowVariable]
hisat2-2.2.1/sse_util.h:314:11: note: Shadowed declaration
hisat2-2.2.1/sse_util.h:218:12: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:736:12: style: Local variable 'row' shadows outer argument [shadowArgument]
hisat2-2.2.1/aligner_bt.h:687:18: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.h:736:12: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:736:24: style: Local variable 'col' shadows outer argument [shadowArgument]
hisat2-2.2.1/aligner_bt.h:688:18: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.h:736:24: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:356:10: style: Local variable 'mod' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:68:9: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:356:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:420:10: style: Local variable 'empty' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_bt.h:602:7: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:420:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:531:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:358:12: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:531:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:963:10: style: Local variable 'empty' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_bt.h:602:7: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:963:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1076:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:903:12: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1076:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1177:9: style: Local variable 'matches' shadows outer function [shadowFunction]
hisat2-2.2.1/mask.h:48:20: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1177:9: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1487:11: style: Local variable 'diag' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:1476:10: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1487:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:337:8: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_bt.cpp:1143:7: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/dp_framer.h:243:12: style: Parameter 'refl' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/dp_framer.h:244:12: style: Parameter 'refr' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_bt.h:589:28: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_bt.cpp:45:16: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_bt.cpp:595:16: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_bt.cpp:1240:12: style: Variable 'b' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_bt.cpp:1696:10: style: Parameter 'niter' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_bt.cpp:515:12: style: Variable 'cur_new' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/aligner_bt.cpp:1061:12: style: Variable 'cur_new' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:93:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:206:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:298:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:794:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1223:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1333:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_bt.cpp:647:12: style: Variable 'xi' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_bt.cpp:670:20: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_bt.cpp:670:39: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::inited_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nrow_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::ncol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nvecrow_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nveccol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::wperv_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::vecshift_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nvecPerCol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::colstride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::rowstride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::qprofStride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::gbarStride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::maxPen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::maxBonus_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::lastIter_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::lastWord_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::bias_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < uint16_t , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_swsse.h:108:2: style: Struct 'SSEMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_swsse.h:409:2: style: Struct 'SSEData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_swsse.cpp:48:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/aligner_swsse.h:233:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse.h:236:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse.cpp:83:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse.cpp:86:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse.cpp:43:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:93:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:195:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:299:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:792:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1208:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1318:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rd_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qu_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdfw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdrc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qufw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qurc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::fw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::refidx_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::reflen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rect_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rff_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdgap_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfgap_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::enable8_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::extend_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::minsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nceil_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse8succ_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse16succ_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltst_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltdo_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw_nuc.h:119:14: style:inconclusive: Technically the member function 'DpBtCandidate::dominatedBy' can be const. [functionConst]
hisat2-2.2.1/aligner_sw.h:338:7: style:inconclusive: Technically the member function 'SwAligner::printResultStacked' can be const. [functionConst]
hisat2-2.2.1/aligner_sw.h:395:7: style:inconclusive: Technically the member function 'SwAligner::merge' can be const. [functionConst]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < DpNucFrame , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < DpNucFrame , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < DpNucFrame , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < std :: pair < unsigned long , unsigned long > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: 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]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < std :: pair < unsigned long , unsigned long > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < DpBtCandidate , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < DpBtCandidate , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < DpBtCandidate , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed2.h:546:15: warning: Assert statement calls a function which may have desired side effects: 'containsEx'. [assertWithSideEffect]
hisat2-2.2.1/aligner_sw.cpp:199:8: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_sw.cpp:332:8: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/ds.h:529:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/ds.h:536:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/random_util.h:50:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:50:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:55:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:55:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::pen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::depth' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::rootpri' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::l2r' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::pri' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::posFlag' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::d' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::topf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::topb' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::botb' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::off5p' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::rid_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::al5pi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::al5pf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::l2r_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::gapadd_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::off5p_i_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::topf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::botf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::topb_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::botb_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::parent_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::pen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::posid_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::len_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1911:2: warning: Member variable 'DescentDriver::minsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1911:2: warning: Member variable 'DescentDriver::maxpen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S::resolveAll' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:693:7: style:inconclusive: Technically the member function 'DescentPosFlags::mmExplore' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:726:7: style:inconclusive: Technically the member function 'DescentPosFlags::rdgExplore' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:759:7: style:inconclusive: Technically the member function 'DescentPosFlags::rfgExplore' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:3354:24: performance:inconclusive: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed2.h:1204:7: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed2.h:3354:24: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed2.h:1219:7: style:inconclusive: Technically the member function 'Descent::collectEdits' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:2027:7: performance:inconclusive: Technically the member function 'DescentDriver::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed2.h:2379:7: performance:inconclusive: Technically the member function 'DescentPartialAlignmentSelector::compileBatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: 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]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < DescentPartialResolvedAlignment , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < DescentPartialResolvedAlignment , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < DescentPartialResolvedAlignment , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < DescentConfig , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < DescentConfig , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < DescentConfig , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < DescentRoot , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < DescentRoot , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < DescentRoot , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/random_util.h:50:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/random_util.h:55:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_seed2.h:1911:2: style: Class 'DescentDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2471:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_sw.h:565:10: style: The scope of the variable 'nrej' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw.cpp:84:2: style: Unsigned expression 'readGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw.cpp:85:2: style: Unsigned expression 'refGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw.cpp:923:18: style: Local variable 'col' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw.cpp:741:10: note: Shadowed declaration
hisat2-2.2.1/aligner_sw.cpp:923:18: note: Shadow variable
hisat2-2.2.1/aligner_sw.cpp:924:18: style: Local variable 'row' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw.cpp:740:10: note: Shadowed declaration
hisat2-2.2.1/aligner_sw.cpp:924:18: note: Shadow variable
hisat2-2.2.1/aligner_sw_nuc.h:54:12: performance: Function parameter 'score_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_sw.cpp:478:16: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_sw.cpp:602:12: style: Variable 'd8' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_sw.cpp:603:12: style: Variable 'd16' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_sw.cpp:745:13: style: Variable 'd' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_sw.cpp:754:13: style: Variable 'd' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_seed2.h:687:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_seed2.h:531:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed2.h:573:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed2.h:3824:9: style: The scope of the variable 'nobranchDepth' can be reduced. [variableScope]
hisat2-2.2.1/group_walk.h:685:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:685:21: note: Shadow variable
hisat2-2.2.1/group_walk.h:716:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:716:21: note: Shadow variable
hisat2-2.2.1/group_walk.h:765:28: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:765:28: note: Shadow variable
hisat2-2.2.1/group_walk.h:811:29: style: Local variable 'n' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:765:21: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:811:29: note: Shadow variable
hisat2-2.2.1/group_walk.h:856:25: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:765:28: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:856:25: note: Shadow variable
hisat2-2.2.1/group_walk.h:1118:52: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1118:52: note: Shadow variable
hisat2-2.2.1/group_walk.h:1199:52: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1199:52: note: Shadow variable
hisat2-2.2.1/group_walk.h:1306:27: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1306:27: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3118:11: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3118:11: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3182:13: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3182:13: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3212:14: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3212:14: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3263:12: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3263:12: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3290:13: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3290:13: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:4132:11: style: Local variable 'nopts' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed2.h:4106:10: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:4132:11: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:838:8: performance: Function parameter 'e_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:840:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:874:8: performance: Function parameter 'e_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:876:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:977:26: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/group_walk.h:1014:16: style: Parameter 'met' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/group_walk.h:1434:17: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_seed2.h:580:39: style: Variable 'map' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/aligner_seed2.h:2341:17: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_seed2.h:2342:16: style: Parameter 'met' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_seed2.h:2404:11: style: Parameter 'rs' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_seed2.h:4136:27: style: Variable 'nopts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:785:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:779:5: note: First condition
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:785:5: note: Second condition
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:607:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:660:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:661:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:662:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:710:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:711:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:712:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1137:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1233:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1392:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1400:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1405:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1451:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1452:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1453:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1508:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1509:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1510:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1511:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1512:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1513:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:690:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:691:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:690:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:416:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:365:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:416:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:412:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:366:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:412:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:884:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:831:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:884:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:880:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:832:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:880:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:187:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:188:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:189:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:190:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:425:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:893:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1794:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:204:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:296:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:968:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1477:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1679:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1331:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:542:18: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1331:17: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:605:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:372:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:605:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:644:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:644:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:648:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:491:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:648:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:708:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:461:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:708:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1135:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:840:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1135:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:155:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/sam.h:1242:9: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
hisat2-2.2.1/aln_sink.h:669:11: warning: Member variable 'AlnSink::numWrappers_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_driver.h:144:2: warning: Member variable 'AlignerDriver::paired_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_driver.h:98:3: performance: Variable 'rootIval_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_driver.h:156:3: performance: Variable 'totsz_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_driver.h:157:3: performance: Variable 'totfmops_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/sam.h:417:26: performance:inconclusive: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:187:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:210:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldNewlineEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:469:26: performance:inconclusive: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:1637:24: performance:inconclusive: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:881:7: performance:inconclusive: Technically the member function 'AlnSink::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:1220:28: style:inconclusive: Technically the member function 'AlnSinkWrap::reportingParams' can be const. [functionConst]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:411:2: style: Class 'ReportingState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/unique.h:106:11: style: The destructor '~BowtieMapq3' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:75:11: note: Virtual destructor in base class
hisat2-2.2.1/unique.h:106:11: note: Destructor in derived class
hisat2-2.2.1/unique.h:111:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:111:16: note: Function in derived class
hisat2-2.2.1/unique.h:181:11: style: The destructor '~BowtieMapq2' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:75:11: note: Virtual destructor in base class
hisat2-2.2.1/unique.h:181:11: note: Destructor in derived class
hisat2-2.2.1/unique.h:186:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:186:16: note: Function in derived class
hisat2-2.2.1/unique.h:441:11: style: The destructor '~BowtieMapq' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:75:11: note: Virtual destructor in base class
hisat2-2.2.1/unique.h:441:11: note: Destructor in derived class
hisat2-2.2.1/unique.h:446:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:446:16: note: Function in derived class
hisat2-2.2.1/aln_sink.h:1539:11: style: The destructor '~AlnSinkSam' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aln_sink.h:687:11: note: Virtual destructor in base class
hisat2-2.2.1/aln_sink.h:1539:11: note: Destructor in derived class
hisat2-2.2.1/aln_sink.h:1547:15: style: The function 'append' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aln_sink.h:701:15: note: Virtual function in base class
hisat2-2.2.1/aln_sink.h:1547:15: note: Function in derived class
hisat2-2.2.1/aligner_driver.h:102:11: style: The destructor '~AlignerDriverRootSelector' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aligner_seed2.h:1828:11: note: Virtual destructor in base class
hisat2-2.2.1/aligner_driver.h:102:11: note: Destructor in derived class
hisat2-2.2.1/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]
hisat2-2.2.1/aligner_seed2.h:1830:15: note: Virtual function in base class
hisat2-2.2.1/aligner_driver.h:104:15: note: Function in derived class
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:187:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:188:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/sam.h:1032:12: style: The statement 'if (snp_first) snp_first=false' is logically equivalent to 'snp_first=false'. [duplicateConditionalAssign]
hisat2-2.2.1/sam.h:1032:33: note: Assignment 'snp_first=false'
hisat2-2.2.1/sam.h:1032:12: note: Condition 'snp_first' is redundant
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:189:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:190:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:430:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:431:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:432:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aln_sink.h:1837:39: style: Condition 'rd1_==NULL' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aln_sink.h:1837:23: note: Assuming that condition 'rd1==NULL' is not redundant
hisat2-2.2.1/aln_sink.h:1834:21: note: Assuming that condition '(rd1_==NULL)==(rd1==NULL)' is not redundant
hisat2-2.2.1/aln_sink.h:1837:39: note: Condition 'rd1_==NULL' is always true
hisat2-2.2.1/unique.h:461:12: style: The scope of the variable 'secbest' can be reduced. [variableScope]
hisat2-2.2.1/aln_sink.h:1736:22: style: The scope of the variable 'ncondiscord_0' can be reduced. [variableScope]
hisat2-2.2.1/unique.h:132:4: style: Unsigned expression 'best_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/unique.h:138:5: style: Unsigned expression 'diff_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aln_sink.h:3037:23: style:inconclusive: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'. [funcArgNamesDifferent]
hisat2-2.2.1/aln_sink.h:1605:15: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
hisat2-2.2.1/aln_sink.h:3037:23: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
hisat2-2.2.1/aln_sink.h:3031:19: style: Parameter 'rso' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/unique.h:61:9: style: Parameter 'inps' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/banded.h:33:7: performance:inconclusive: Technically the member function 'BandedSseAligner::init' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/banded.h:44:7: performance:inconclusive: Technically the member function 'BandedSseAligner::nextAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/banded.h:34:11: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/banded.h:37:11: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/unique.h:229:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/unique.h:461:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/sstring.h:1798:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1842:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1858:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1870:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1950:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:1959:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2011:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/sstring.h:2101:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:154:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/diff_sample.h:688:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:783:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:777:5: note: First condition
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:783:5: note: Second condition
hisat2-2.2.1/aln_sink.cpp:76:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.cpp:118:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.cpp:173:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.cpp:241:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aln_sink.cpp:333:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:599:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:652:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:653:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:654:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:705:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:707:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1122:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1218:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1377:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1385:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1390:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1436:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1437:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1438:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1493:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1494:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1495:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1496:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1497:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1498:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:685:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:686:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:685:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:414:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:375:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:414:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:879:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:840:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:879:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:184:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:185:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:186:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:187:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:423:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:888:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:218:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:308:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:974:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1478:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1688:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1781:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1316:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:533:18: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1316:17: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:597:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:373:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:597:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:636:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:636:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:640:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:487:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:640:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:703:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:459:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:703:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1120:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:838:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1120:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:152:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:184:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:185:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:186:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:187:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:428:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:429:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:430:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::cs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::printcs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::zero_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning:inconclusive: Member variable 'SStringExpandable::zeroT_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::len_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::sz_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/ls.h:43:1: style: The class 'LarssonSadakane' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
hisat2-2.2.1/sstring.h:1880:7: style:inconclusive: Technically the member function 'SStringExpandable::operator==' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1887:7: style:inconclusive: Technically the member function 'SStringExpandable::operator!=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1894:7: style:inconclusive: Technically the member function 'SStringExpandable::operator<' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1901:7: style:inconclusive: Technically the member function 'SStringExpandable::operator>' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1908:7: style:inconclusive: Technically the member function 'SStringExpandable::operator<=' can be const. [functionConst]
hisat2-2.2.1/sstring.h:1915:7: style:inconclusive: Technically the member function 'SStringExpandable::operator>=' can be const. [functionConst]
hisat2-2.2.1/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hisat2-2.2.1/filebuf.h:550:3: warning: Class 'OutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/filebuf.h:550:3: warning: Class 'OutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const std::basic_string<T>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3034:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2868. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2868:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3034:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:3026:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2870. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2870:5: note: Calling installChars
hisat2-2.2.1/sstring.h:3026:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3012:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2889. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2889:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3012:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2998:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2891. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2891:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2998:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2983:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2894. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2894:4: note: Calling install
hisat2-2.2.1/sstring.h:2983:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,bool chars=false,bool colors=false)' at line 2907. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2907:3: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3041:7: warning: The class 'SDnaStringExpandable' defines member function with name 'set' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1789:7: note: Parent function 'SStringExpandable::set'
hisat2-2.2.1/sstring.h:3041:7: note: Derived function 'SDnaStringExpandable::set'
hisat2-2.2.1/sstring.h:3089:21: warning: The class 'SDnaStringExpandable' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1817:11: note: Parent function 'SStringExpandable::operator[]'
hisat2-2.2.1/sstring.h:3089:21: note: Derived function 'SDnaStringExpandable::operator[]'
hisat2-2.2.1/sstring.h:3096:21: warning: The class 'SDnaStringExpandable' defines member function with name 'get' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1833:11: note: Parent function 'SStringExpandable::get'
hisat2-2.2.1/sstring.h:3096:21: note: Derived function 'SDnaStringExpandable::get'
hisat2-2.2.1/sstring.h:3287:7: warning: The class 'SDnaMaskString' defines member function with name 'set' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1789:7: note: Parent function 'SStringExpandable::set'
hisat2-2.2.1/sstring.h:3287:7: note: Derived function 'SDnaMaskString::set'
hisat2-2.2.1/sstring.h:3335:14: warning: The class 'SDnaMaskString' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1817:11: note: Parent function 'SStringExpandable::operator[]'
hisat2-2.2.1/sstring.h:3335:14: note: Derived function 'SDnaMaskString::operator[]'
hisat2-2.2.1/sstring.h:3342:8: warning: The class 'SDnaMaskString' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1825:5: note: Parent function 'SStringExpandable::operator[]'
hisat2-2.2.1/sstring.h:3342:8: note: Derived function 'SDnaMaskString::operator[]'
hisat2-2.2.1/sstring.h:3349:14: warning: The class 'SDnaMaskString' defines member function with name 'get' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
hisat2-2.2.1/sstring.h:1833:11: note: Parent function 'SStringExpandable::get'
hisat2-2.2.1/sstring.h:3349:14: note: Derived function 'SDnaMaskString::get'
hisat2-2.2.1/sstring.h:2910:11: style: The destructor '~SDnaStringExpandable' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:1710:11: note: Virtual destructor in base class
hisat2-2.2.1/sstring.h:2910:11: note: Destructor in derived class
hisat2-2.2.1/sstring.h:3190:11: style: The destructor '~SDnaMaskString' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:1710:11: note: Virtual destructor in base class
hisat2-2.2.1/sstring.h:3190:11: note: Destructor in derived class
hisat2-2.2.1/ls.h:127:38: style: Variable 'pn' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/ds.cpp:44:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/dp_framer.cpp:92:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/dp_framer.cpp:192:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/dp_framer.cpp:306:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:33:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:71:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:93:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:133:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:145:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:162:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:237:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bit_packed_array.cpp:280:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:959:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:953:5: note: First condition
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:959:5: note: Second condition
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:703:33: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:705:12: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:892:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:894:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1516:33: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:755:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:756:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:757:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:805:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:807:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1515:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1554:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1743:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1751:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1756:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1806:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1807:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1808:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1863:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1864:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1865:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1866:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1867:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1868:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:785:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:786:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:785:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:425:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:365:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:425:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:422:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:366:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:422:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:910:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:374:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:910:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1055:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1005:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1055:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1052:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1006:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1052:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1373:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1012:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1373:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:185:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:186:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:187:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:188:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1064:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2153:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1489:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1489. [zerodivcond]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1488:2: note: Assuming that condition '(bonus)>(0)' is not redundant
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1489:49: note: Division by zero
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1677:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:524:18: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1677:17: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:694:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:634:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:694:9: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:739:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:739:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:743:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:563:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:743:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:803:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:471:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:803:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:153:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:185:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:186:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:187:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:188:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:439:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:441:20: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:442:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat.h:612:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/radix_sort.h:167:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:868:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2015:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2045:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:166:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:223:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3151:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3240:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3492:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:3627:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4059:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4716:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5155:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:5752:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6608:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6692:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6791:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6831:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6898:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.cpp:50:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:86:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:152:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:229:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:325:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:379:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:404:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:446:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:471:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/edit.cpp:486:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT::reversed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB::get_alt_range'
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB::get_alt_range'
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph::getNextEdgeRange'
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph::getNextEdgeRange'
hisat2-2.2.1/gbwt_graph.h:266:13: performance: Variable 'id' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < uint32_t , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:3151:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4949:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gfm.h:6359:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2873. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2873:4: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/gfm.cpp:45:37: style:inconclusive: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:6972:37: note: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'.
hisat2-2.2.1/gfm.cpp:45:37: note: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'.
hisat2-2.2.1/hisat2_build.cpp:535:19: debug: Failed to instantiate template "HGFM". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/hisat2_build.cpp:453:20: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/hisat2_build_main.cpp:63:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build_main.cpp:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2_build_main.cpp:54:46: note: Assuming allocation function fails
hisat2-2.2.1/hisat2_build_main.cpp:54:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
hisat2-2.2.1/hisat2_build_main.cpp:56:5: note: Null pointer dereference
hisat2-2.2.1/hisat2_build_main.cpp:54:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:965:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:958:5: note: First condition
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:965:5: note: Second condition
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:710:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:710:40: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:711:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:902:10: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:902:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:903:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:761:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:762:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:763:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:810:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:812:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1517:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1554:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1747:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1755:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1760:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1806:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1807:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1808:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1863:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1864:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1865:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1866:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1867:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1868:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:790:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:791:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:790:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::item_bit_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::elm_bit_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_bit_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_bit_mask_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::cur_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::sz_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::block_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.cpp:229:22: style: Unused private function: 'BitPackedArray::expand' [unusedPrivateFunction]
hisat2-2.2.1/bit_packed_array.h:82:10: note: Unused private function: 'BitPackedArray::expand'
hisat2-2.2.1/bit_packed_array.cpp:229:22: note: Unused private function: 'BitPackedArray::expand'
hisat2-2.2.1/bit_packed_array.h:70:21: performance:inconclusive: Technically the member function 'BitPackedArray::bitToMask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/bit_packed_array.cpp:187:22: style:inconclusive: Technically the member function 'BitPackedArray::setItem' can be const. [functionConst]
hisat2-2.2.1/bit_packed_array.h:76:10: note: Technically the member function 'BitPackedArray::setItem' can be const.
hisat2-2.2.1/bit_packed_array.cpp:187:22: note: Technically the member function 'BitPackedArray::setItem' can be const.
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint64_t * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint64_t * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint64_t * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:440:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:378:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:440:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:919:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:386:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:919:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1059:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1014:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1059:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1378:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1020:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1378:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:199:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:200:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:201:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:202:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1073:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2147:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1490:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1490. [zerodivcond]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1489:2: note: Assuming that condition '(bonus)>(0)' is not redundant
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1490:49: note: Division by zero
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1686:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:515:18: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1686:17: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/bit_packed_array.cpp:65:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/bit_packed_array.cpp:126:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:701:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:642:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:701:9: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:745:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:745:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:749:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:569:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:749:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:808:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:488:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:808:16: note: Shadow variable
hisat2-2.2.1/bit_packed_array.cpp:50:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:51:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:52:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:53:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:54:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:56:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:57:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:59:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:63:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:88:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:92:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:95:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:98:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:101:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:106:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:111:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:115:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bit_packed_array.cpp:123:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:167:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/bit_packed_array.cpp:31:39: style:inconclusive: Function 'get' argument 1 names different: declaration 'idx' definition 'index'. [funcArgNamesDifferent]
hisat2-2.2.1/bit_packed_array.h:46:27: note: Function 'get' argument 1 names different: declaration 'idx' definition 'index'.
hisat2-2.2.1/bit_packed_array.cpp:31:39: note: Function 'get' argument 1 names different: declaration 'idx' definition 'index'.
hisat2-2.2.1/bit_packed_array.cpp:165:46: style: Parameter 'block' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/edit.cpp:393:9: style:inconclusive: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:363:10: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
hisat2-2.2.1/edit.cpp:393:9: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
hisat2-2.2.1/edit.cpp:394:9: style:inconclusive: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:364:10: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
hisat2-2.2.1/edit.cpp:394:9: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
hisat2-2.2.1/edit.cpp:468:32: style:inconclusive: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:288:34: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:468:32: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:485:32: style:inconclusive: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:293:34: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:485:32: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/hi_aligner.h:799:46: debug: Failed to instantiate template "SStringExpandable". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/hgfm.h:357:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:779:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1714:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:435:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:448:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _repeatLens [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:457:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:470:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:475:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:160:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT2_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:296:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:426:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:464:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:269:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:546:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:693:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _in1Str [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:965:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _verbose [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:86:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _in1 [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:163:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _gh [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:263:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:268:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1806:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PathNodeFrom [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1820:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable temp_nodes [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1866:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable generation [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1900:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable generation [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1914:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable generation [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1959:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable generation [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2156:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable generation [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2278:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodes [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2376:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sorted [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1840:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1991:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _in5Str [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:2479:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _verbose [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:93:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _in1Str [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:184:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _gh [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:313:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:318:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1150:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _offsLen [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/word_io.h:332:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:199:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:200:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:201:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:202:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:459:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:460:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:461:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hgfm.h:1562:10: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/hisat2_main.cpp:62:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_main.cpp:55:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2_main.cpp:53:46: note: Assuming allocation function fails
hisat2-2.2.1/hisat2_main.cpp:53:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
hisat2-2.2.1/hisat2_main.cpp:55:5: note: Null pointer dereference
hisat2-2.2.1/hisat2_main.cpp:53:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:66:12: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:66:12: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:69:5: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
hisat2-2.2.1/hisat2lib/ht2_index.cpp:69:5: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:70:5: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
hisat2-2.2.1/hisat2lib/ht2_index.cpp:70:5: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:73:16: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
hisat2-2.2.1/hisat2lib/ht2_index.cpp:73:16: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:9: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:9: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:32: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:32: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: note: Null pointer addition
hisat2-2.2.1/hisat2lib/ht2_index.cpp:33:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:49:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:51: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:211:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:184:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:208:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:162:55: style: Parameter 'options' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:36:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:93:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:90:5: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:88: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: note: Assignment 'result=(struct ht2_repeat_expand_result*)malloc(result_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:90:5: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:95:9: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:88: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: note: Assignment 'result=(struct ht2_repeat_expand_result*)malloc(result_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:95:9: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:96:9: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:88: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: note: Assignment 'result=(struct ht2_repeat_expand_result*)malloc(result_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:96:9: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:97:9: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:88: note: Assuming allocation function fails
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: note: Assignment 'result=(struct ht2_repeat_expand_result*)malloc(result_size)', assigned value is 0
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:97:9: note: Null pointer dereference
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:32:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:58:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:316:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HT2_OK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:352:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HT2_OK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:371:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JNI_OK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:121:39: style: Condition 'GetInteger(env,valueObj,&value)<0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:121:15: note: Calling function 'GetInteger' returns 0
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:121:39: note: Condition 'GetInteger(env,valueObj,&value)<0' is always false
hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:136:58: style: Parameter 'opts' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/hisat2lib/pymodule/ht2module.c:203:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Py_None [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/pymodule/ht2module.c:259:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HT2_OK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2lib/pymodule/ht2module.c:297:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HT2_OK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat_main.cpp:63:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat_main.cpp:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
hisat2-2.2.1/hisat2_repeat_main.cpp:54:46: note: Assuming allocation function fails
hisat2-2.2.1/hisat2_repeat_main.cpp:54:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
hisat2-2.2.1/hisat2_repeat_main.cpp:56:5: note: Null pointer dereference
hisat2-2.2.1/hisat2_repeat_main.cpp:54:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:528:15: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/ival_list.h:62:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ival_list.h:94:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ival_list.h:147:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ival_list.h:182:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ival_list.h:234:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ival_list.h:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Interval , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Interval , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Interval , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Coord , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Coord , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Coord , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < EIvalMergeList , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < EIvalMergeList , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < EIvalMergeList , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/li_hla/alignments.hpp:30:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/li_hla/alignments.hpp:105:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/li_hla/main.cpp:106:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::fpSam' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::fileName' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::segments' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::segCnt' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:67:7: style:inconclusive: Technically the member function 'Alignments::IsOpened' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:160:6: style:inconclusive: Technically the member function 'Alignments::GetChromId' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:181:6: style:inconclusive: Technically the member function 'Alignments::GetChromLength' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:186:7: style:inconclusive: Technically the member function 'Alignments::GetMatePosition' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:208:7: style:inconclusive: Technically the member function 'Alignments::IsReverse' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:215:7: style:inconclusive: Technically the member function 'Alignments::IsMateReverse' can be const. [functionConst]
hisat2-2.2.1/li_hla/main.cpp:116:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
hisat2-2.2.1/li_hla/main.cpp:114:12: note: Assuming allocation function fails
hisat2-2.2.1/li_hla/main.cpp:114:12: note: Assignment 'fp=fopen(buffer,"r")', assigned value is 0
hisat2-2.2.1/li_hla/main.cpp:116:43: note: Null pointer dereference
hisat2-2.2.1/li_hla/main.cpp:171:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
hisat2-2.2.1/li_hla/main.cpp:163:12: note: Assuming allocation function fails
hisat2-2.2.1/li_hla/main.cpp:163:12: note: Assignment 'fp=fopen(buffer,"r")', assigned value is 0
hisat2-2.2.1/li_hla/main.cpp:171:43: note: Null pointer dereference
hisat2-2.2.1/li_hla/main.cpp:208:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
hisat2-2.2.1/li_hla/main.cpp:206:12: note: Assuming allocation function fails
hisat2-2.2.1/li_hla/main.cpp:206:12: note: Assignment 'fp=fopen(buffer,"r")', assigned value is 0
hisat2-2.2.1/li_hla/main.cpp:208:43: note: Null pointer dereference
hisat2-2.2.1/li_hla/alignments.hpp:140:12: style: The scope of the variable 'mPos' can be reduced. [variableScope]
hisat2-2.2.1/li_hla/main.cpp:443:6: style: The scope of the variable 'maxk' can be reduced. [variableScope]
hisat2-2.2.1/li_hla/main.cpp:303:8: style: Local variable 'size' shadows outer variable [shadowVariable]
hisat2-2.2.1/li_hla/main.cpp:292:7: note: Shadowed declaration
hisat2-2.2.1/li_hla/main.cpp:303:8: note: Shadow variable
hisat2-2.2.1/li_hla/alignments.hpp:49:19: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/li_hla/alignments.hpp:76:13: style: Variable 'rawCigar' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/li_hla/main.cpp:149:42: performance: Searching before insertion is not necessary. Instead of 'positionToSnp[info.position+p]=tmpList' consider using 'positionToSnp.try_emplace(info.position+p, tmpList);'. [stlFindInsert]
hisat2-2.2.1/li_hla/main.cpp:225:35: performance: Searching before insertion is not necessary. Instead of 'alleleNameToId[fields[i]]=k' consider using 'alleleNameToId.try_emplace(fields[i], k);'. [stlFindInsert]
hisat2-2.2.1/li_hla/main.cpp:140:22: warning: Uninitialized variable: info.nucleotide [uninitvar]
hisat2-2.2.1/li_hla/main.cpp:124:18: note: Assuming condition is true
hisat2-2.2.1/li_hla/main.cpp:140:22: note: Uninitialized variable: info.nucleotide
hisat2-2.2.1/li_hla/main.cpp:140:22: error: Uninitialized struct member: info.nucleotide [uninitStructMember]
hisat2-2.2.1/li_hla/main.cpp:14:6: style: struct member '_compatible::weight' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:28:7: style: struct member '_mdComponent::type' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:29:6: style: struct member '_mdComponent::length' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:30:6: style: struct member '_mdComponent::num' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/alignments.hpp:117:11: style: Variable 'num' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/alignments.hpp:139:8: style: Variable 'mChrId' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/main.cpp:443:11: style: Variable 'maxk' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/main.cpp:452:10: style: Variable 'maxk' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2_inspect.cpp:80:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT2_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:123:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:148:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:182:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:218:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:255:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:660:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:734:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:611:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:565:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:493:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:386:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:340:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:1767:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2082:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nthreads [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:374:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nthreads [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/msvcc/codeStubs/getopt.c:689:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/msvcc/codeStubs/getopt.c:528:60: style:inconclusive: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:134:21: note: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'.
hisat2-2.2.1/msvcc/codeStubs/getopt.c:528:60: note: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'.
hisat2-2.2.1/msvcc/codeStubs/getopt.c:784:11: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:69:57: style:inconclusive: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:126:66: note: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:69:57: note: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:35: style:inconclusive: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:127:32: note: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:35: note: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:54: style:inconclusive: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:127:47: note: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:54: note: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:81:60: style:inconclusive: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:129:21: note: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:81:60: note: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:40: style:inconclusive: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:130:37: note: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:40: note: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:59: style:inconclusive: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:130:52: note: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:59: note: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp:51:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _timezone [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp:27:14: style: The scope of the variable 'tzflag' can be reduced. [variableScope]
hisat2-2.2.1/bp_aligner.h:133:5: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
hisat2-2.2.1/outq.cpp:30:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/outq.cpp:54:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM::mmFile5_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM::mmFile6_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1606:9: performance: Variable '_in5Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/hgfm.h:1607:9: performance: Variable '_in6Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:328:9: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:329:9: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/diff_sample.h:509:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < SString < char > >::print' can be const. [functionConst]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < uint32_t , 6 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < pair < uint32_t , uint32_t > , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/blockwise_sa.h:352:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < SString < char > >(const SString < char >&__text,uint32_t __bucketSz,int __nthreads,uint32_t __dcV,uint32_t __seed=0,bool __sanityCheck=false,bool __passMemExc=false,bool __verbose=false,std::string base_fname="",ostream&__logger=cout)' at line 206. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/blockwise_sa.h:206:29: note: Calling reset
hisat2-2.2.1/blockwise_sa.h:352:15: note: reset is a virtual function
hisat2-2.2.1/rfm.h:262:7: warning: The class 'LocalRFM < uint32_t >' defines member function with name 'sanityCheckAll' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:6830:20: note: Parent function 'GFM < uint32_t >::sanityCheckAll'
hisat2-2.2.1/rfm.h:262:7: note: Derived function 'LocalRFM < uint32_t >::sanityCheckAll'
hisat2-2.2.1/blockwise_sa.h:208:6: style: The destructor '~KarkkainenBlockwiseSA < SString < char > >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:85:11: note: Virtual destructor in base class
hisat2-2.2.1/blockwise_sa.h:208:6: note: Destructor in derived class
hisat2-2.2.1/hisat2_build.cpp:710:13: style: Condition 'optind>=argc' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2_build.cpp:702:13: note: Assuming that condition 'optind>=argc' is not redundant
hisat2-2.2.1/hisat2_build.cpp:710:13: note: Condition 'optind>=argc' is always false
hisat2-2.2.1/hgfm.h:1815:26: style: Condition 'tParam.last' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hgfm.h:1806:11: note: Assuming that condition '!tParam.last' is not redundant
hisat2-2.2.1/hgfm.h:1815:26: note: Condition 'tParam.last' is always false
hisat2-2.2.1/hgfm.h:1388:8: style: Condition 'loadFtab' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hgfm.h:1366:6: note: Assuming that condition 'loadFtab' is not redundant
hisat2-2.2.1/hgfm.h:1388:8: note: Condition 'loadFtab' is always true
hisat2-2.2.1/hgfm.h:395:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:417:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:705:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:823:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:843:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:1064:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hisat2_build.cpp:826:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:1205:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:582:15: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:585:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:585:63: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1002:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/rfm.h:533:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:445:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1805:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:2211:63: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:2335:33: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1196:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1243:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1293:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1296:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1379:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1409:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1482:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1513:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1515:20: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1524:19: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1490:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/word_io.h:331:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/pat.h:68:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:432:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:769:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:889:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:985:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:1199:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:1322:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:1444:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:1519:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.h:1598:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:67:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:205:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:270:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:317:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:356:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:469:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:671:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:748:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:876:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1179:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1247:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1425:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1462:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1506:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1514:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1520:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_build.cpp:281:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hgfm.h:2023:13: style: The scope of the variable 'cumlen' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1209:7: style: The scope of the variable 'shmemLeader' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1117:58: style:inconclusive: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'. [funcArgNamesDifferent]
hisat2-2.2.1/hgfm.h:297:11: note: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'.
hisat2-2.2.1/hgfm.h:1117:58: note: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'.
hisat2-2.2.1/gfm.h:4367:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4367:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4370:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4370:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6479:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6479:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6482:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6482:13: note: Shadow variable
hisat2-2.2.1/gfm.h:5975:14: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5975:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5984:14: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5984:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:1775:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:1775:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:372:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:372:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:880:13: style: Local variable 'nthreads' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:77:12: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:880:13: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:893:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:893:16: note: Shadow variable
hisat2-2.2.1/hgfm.h:2269:45: style: Local variable 'alt' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2265:34: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2269:45: note: Shadow variable
hisat2-2.2.1/hgfm.h:2303:51: style: Local variable 'haplotype' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2299:40: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2303:51: note: Shadow variable
hisat2-2.2.1/hgfm.h:2310:41: style: Local variable 'alt_i' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2267:29: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2310:41: note: Shadow variable
hisat2-2.2.1/hgfm.h:2583:10: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2583:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:2585:10: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2585:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:2589:10: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2589:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:1270:8: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:1209:7: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:1270:8: note: Shadow variable
hisat2-2.2.1/hgfm.h:391:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:413:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:701:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:819:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:839:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:1060:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/rfm.h:459:21: style: Variable 'ref' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hisat2_build.cpp:821:32: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/rfm.h:45:22: style: Parameter 'bytesRead' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/rfm.h:46:22: style: Parameter 'bytesRead2' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hgfm.h:1116:62: style: Parameter 'bytesRead2' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hgfm.h:1202:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:1284:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:1433:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hgfm.h:1452:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/gbwt_graph.h:1519:51: style: Parameter 'a' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gbwt_graph.h:1523:50: style: Parameter 'a' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/gbwt_graph.h:1569:49: style: Parameter 'a' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/aligner_metrics.h:138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_seed.h:1790:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pe.h:118:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pe.h:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:235:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:259:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:599:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:888:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:1061:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:1322:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/aligner_sw_driver.h:1970:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:63:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:85:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2670:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:778:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:807:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT2_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:1019:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:1079:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:1112:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:1804:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:2937:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3025:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3043:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3061:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3080:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3234:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3680:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2.cpp:3712:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/spliced_aligner.h:132:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/spliced_aligner.h:358:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:4168:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:4693:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:4883:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5027:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5223:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5506:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5603:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5796:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5882:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:5978:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6080:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6288:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6316:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6388:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6643:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6792:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6902:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:6918:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:748:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:842:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:884:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:956:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:986:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:1030:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:1285:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:1393:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:1444:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2051:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2268:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2403:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2491:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2554:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:2795:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:3571:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:3643:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:3735:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:236:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:248:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:270:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:275:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:280:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:309:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:325:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _len [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:337:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:342:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:355:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:365:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _bwoff [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:135:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:174:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:179:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hi_aligner.h:188:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/rfm.h:697:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gbwt_graph.h:2299:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verbose [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3214:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3231:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3254:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3272:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3294:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3341:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3352:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ds.h:3362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:232:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:238:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:342:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:361:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:370:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.h:806:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:181:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT2_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:301:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:355:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:513:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:281:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_repeat.cpp:295:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::_nrefs' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::_nlocalGFMs' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::mmFile5_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::mmFile6_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < uint16_t >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offMask' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offsLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offsSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_lineSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideGbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideGbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numSides' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numLines' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtTotLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtTotSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numNodes' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::tid' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::toff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::joinedOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:50:5: warning: Member variable 'RepeatCoord < uint16_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint16_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint16_t >::reversed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange'
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange'
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint16_t >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint16_t >::get_alt_range'
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint16_t >::get_alt_range'
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < uint16_t >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < uint16_t >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < uint16_t >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < uint16_t >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < uint16_t >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < uint16_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < uint16_t >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < uint16_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < uint16_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < uint16_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < uint16_t , 6 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < pair < uint16_t , uint16_t > , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hgfm.h:312:7: warning: The class 'LocalGFM < uint16_t , uint32_t >' defines member function with name 'sanityCheckAll' also defined in its parent class 'GFM < uint16_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:6830:20: note: Parent function 'GFM < uint16_t >::sanityCheckAll'
hisat2-2.2.1/hgfm.h:312:7: note: Derived function 'LocalGFM < uint16_t , uint32_t >::sanityCheckAll'
hisat2-2.2.1/hgfm.h:1659:7: warning: The class 'HGFM < uint32_t , uint16_t >' defines member function with name 'loadIntoMemory' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:2525:7: note: Parent function 'GFM < uint32_t >::loadIntoMemory'
hisat2-2.2.1/hgfm.h:1659:7: note: Derived function 'HGFM < uint32_t , uint16_t >::loadIntoMemory'
hisat2-2.2.1/hgfm.h:1694:7: warning: The class 'HGFM < uint32_t , uint16_t >' defines member function with name 'evictFromMemory' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:2548:7: note: Parent function 'GFM < uint32_t >::evictFromMemory'
hisat2-2.2.1/hgfm.h:1694:7: note: Derived function 'HGFM < uint32_t , uint16_t >::evictFromMemory'
hisat2-2.2.1/hgfm.h:1703:7: warning: The class 'HGFM < uint32_t , uint16_t >' defines member function with name 'sanityCheckAll' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:6830:20: note: Parent function 'GFM < uint32_t >::sanityCheckAll'
hisat2-2.2.1/hgfm.h:1703:7: note: Derived function 'HGFM < uint32_t , uint16_t >::sanityCheckAll'
hisat2-2.2.1/pe.cpp:47:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pe.cpp:179:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:6866:9: style: Comparing expression of type 'unsigned short' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/gbwt_graph.h:383:38: style: Comparing expression of type 'unsigned short' against value 65536. Condition is always false. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hisat2_inspect.cpp:617:39: style: Condition 'entireReverse' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2_inspect.cpp:585:23: note: Assignment 'entireReverse=false', assigned value is 0
hisat2-2.2.1/hisat2_inspect.cpp:617:39: note: Condition 'entireReverse' is always false
hisat2-2.2.1/hisat2_inspect.cpp:220:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hgfm.h:1513:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/pe.cpp:182:2: style: Unsigned expression 'minfrag_' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/pat.cpp:701:44: 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]
hisat2-2.2.1/pat.cpp:698:38: note: Assuming that condition 'c!=-1' is not redundant
hisat2-2.2.1/pat.cpp:701:44: note: Invalid argument
hisat2-2.2.1/pat.h:1216:2: warning: Member variable 'FastaContinuousPatternSource::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/pat.h:1330:15: style: Virtual function 'resetForNextFile' is called from constructor 'FastaContinuousPatternSource(const EList < string , 128 >&infiles,const PatternParams&p)' at line 1222. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/pat.h:1222:3: note: Calling resetForNextFile
hisat2-2.2.1/pat.h:1330:15: note: resetForNextFile is a virtual function
hisat2-2.2.1/pat.h:995:7: warning: The class 'FastaPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:995:7: note: Derived variable 'FastaPatternSource::first_'
hisat2-2.2.1/pat.h:1465:7: warning: The class 'FastqPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:1465:7: note: Derived variable 'FastqPatternSource::first_'
hisat2-2.2.1/pat.h:1619:7: warning: The class 'RawPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:1619:7: note: Derived variable 'RawPatternSource::first_'
hisat2-2.2.1/pat.h:592:2: style: Class 'WrappedPatternSourcePerThread' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/pat.h:619:2: style: Class 'WrappedPatternSourcePerThreadFactory' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/pat.h:361:11: style: The destructor '~PairedSoloPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:282:11: note: Virtual destructor in base class
hisat2-2.2.1/pat.h:361:11: note: Destructor in derived class
hisat2-2.2.1/pat.h:368:15: style: The function 'addWrapper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:284:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:368:15: note: Function in derived class
hisat2-2.2.1/pat.h:378:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:285:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:378:15: note: Function in derived class
hisat2-2.2.1/pat.h:390:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:287:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:390:15: note: Function in derived class
hisat2-2.2.1/pat.h:403:33: style: The function 'readCnt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:297:33: note: Virtual function in base class
hisat2-2.2.1/pat.h:403:33: note: Function in derived class
hisat2-2.2.1/pat.h:444:11: style: The destructor '~PairedDualPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:282:11: note: Virtual destructor in base class
hisat2-2.2.1/pat.h:444:11: note: Destructor in derived class
hisat2-2.2.1/pat.h:454:15: style: The function 'addWrapper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:284:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:454:15: note: Function in derived class
hisat2-2.2.1/pat.h:467:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:285:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:467:15: note: Function in derived class
hisat2-2.2.1/pat.h:482:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:287:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:482:15: note: Function in derived class
hisat2-2.2.1/pat.h:495:33: style: The function 'readCnt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:297:33: note: Virtual function in base class
hisat2-2.2.1/pat.h:495:33: note: Function in derived class
hisat2-2.2.1/pat.h:602:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:523:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:602:15: note: Function in derived class
hisat2-2.2.1/pat.h:625:34: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:562:34: note: Virtual function in base class
hisat2-2.2.1/pat.h:625:34: note: Function in derived class
hisat2-2.2.1/pat.h:633:42: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:563:42: note: Virtual function in base class
hisat2-2.2.1/pat.h:633:42: note: Function in derived class
hisat2-2.2.1/pat.h:715:11: style: The destructor '~VectorPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:155:11: note: Virtual destructor in base class
hisat2-2.2.1/pat.h:715:11: note: Destructor in derived class
hisat2-2.2.1/pat.h:717:15: style: The function 'nextReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:216:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:717:15: note: Function in derived class
hisat2-2.2.1/pat.h:727:15: style: The function 'nextReadPairImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:200:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:727:15: note: Function in derived class
hisat2-2.2.1/pat.h:736:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:224:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:736:15: note: Function in derived class
hisat2-2.2.1/pat.h:777:11: style: The destructor '~BufferedFilePatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:155:11: note: Virtual destructor in base class
hisat2-2.2.1/pat.h:777:11: note: Destructor in derived class
hisat2-2.2.1/pat.h:786:15: style: The function 'nextReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:216:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:786:15: note: Function in derived class
hisat2-2.2.1/pat.h:816:15: style: The function 'nextReadPairImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:200:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:816:15: note: Function in derived class
hisat2-2.2.1/pat.h:851:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:224:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:851:15: note: Function in derived class
hisat2-2.2.1/pat.h:943:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:943:15: note: Function in derived class
hisat2-2.2.1/pat.h:967:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:967:15: note: Function in derived class
hisat2-2.2.1/pat.h:975:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:975:15: note: Function in derived class
hisat2-2.2.1/pat.h:990:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:990:15: note: Function in derived class
hisat2-2.2.1/pat.h:1042:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1042:15: note: Function in derived class
hisat2-2.2.1/pat.h:1050:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1050:15: note: Function in derived class
hisat2-2.2.1/pat.h:1179:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1179:15: note: Function in derived class
hisat2-2.2.1/pat.h:1189:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1189:15: note: Function in derived class
hisat2-2.2.1/pat.h:1225:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1225:15: note: Function in derived class
hisat2-2.2.1/pat.h:1233:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1233:15: note: Function in derived class
hisat2-2.2.1/pat.h:1313:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1313:15: note: Function in derived class
hisat2-2.2.1/pat.h:1330:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1330:15: note: Function in derived class
hisat2-2.2.1/pat.h:1373:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1373:15: note: Function in derived class
hisat2-2.2.1/pat.h:1426:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1426:15: note: Function in derived class
hisat2-2.2.1/pat.h:1434:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1434:15: note: Function in derived class
hisat2-2.2.1/pat.h:1449:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1449:15: note: Function in derived class
hisat2-2.2.1/pat.h:1485:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1485:15: note: Function in derived class
hisat2-2.2.1/pat.h:1493:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1493:15: note: Function in derived class
hisat2-2.2.1/pat.h:1588:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1588:15: note: Function in derived class
hisat2-2.2.1/pat.h:1603:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1603:15: note: Function in derived class
hisat2-2.2.1/pat.cpp:765:18: style: The comparison 'qc < 0' is always false. [knownConditionTrueFalse]
hisat2-2.2.1/pat.cpp:732:14: note: 'qc' is assigned value '0' here.
hisat2-2.2.1/pat.cpp:765:18: note: The comparison 'qc < 0' is always false.
hisat2-2.2.1/pat.cpp:776:20: style: The comparison 'qc < 0' is always false. [knownConditionTrueFalse]
hisat2-2.2.1/pat.cpp:732:14: note: 'qc' is assigned value '0' here.
hisat2-2.2.1/pat.cpp:776:20: note: The comparison 'qc < 0' is always false.
hisat2-2.2.1/pat.cpp:746:5: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:744:5: note: c is assigned
hisat2-2.2.1/pat.cpp:746:5: note: c is overwritten
hisat2-2.2.1/pat.cpp:1141:4: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:1133:6: note: c is assigned
hisat2-2.2.1/pat.cpp:1141:4: note: c is overwritten
hisat2-2.2.1/pat.cpp:1141:4: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:1135:6: note: c is assigned
hisat2-2.2.1/pat.cpp:1141:4: note: c is overwritten
hisat2-2.2.1/pat.h:987:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1201:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1324:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1446:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1600:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/presets.cpp:85:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/pat.cpp:1356:6: style: The scope of the variable 'c' can be reduced. [variableScope]
hisat2-2.2.1/pat.cpp:718:21: style: Checking if unsigned expression 'r.qual.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/pat.cpp:490:15: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:466:13: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:490:15: note: Shadow variable
hisat2-2.2.1/pat.cpp:1008:9: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:859:6: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:1008:9: note: Shadow variable
hisat2-2.2.1/pat.cpp:1461:10: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:1454:6: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:1461:10: note: Shadow variable
hisat2-2.2.1/pat.cpp:929:12: style: Variable 'trim5' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/pat.cpp:1356:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < std :: pair < int , std :: string > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: 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]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < std :: pair < int , std :: string > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/presets.h:57:11: style: The destructor '~PresetsV0' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/presets.h:39:11: note: Virtual destructor in base class
hisat2-2.2.1/presets.h:57:11: note: Destructor in derived class
hisat2-2.2.1/presets.h:59:15: style: The function 'apply' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/presets.h:41:15: note: Virtual function in base class
hisat2-2.2.1/presets.h:59:15: note: Function in derived class
hisat2-2.2.1/presets.h:64:23: style: The function 'name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/presets.h:46:23: note: Virtual function in base class
hisat2-2.2.1/presets.h:64:23: note: Function in derived class
hisat2-2.2.1/hisat2_inspect.cpp:135:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2_inspect.cpp:283:13: style: The scope of the variable 'tlen' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1726:17: style: The scope of the variable 'tidx' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1809:34: style: Checking if unsigned expression 'tParam.s.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hgfm.h:1823:34: style: Checking if unsigned expression 'tParam.s.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/hisat2_inspect.cpp:419:25: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_inspect.cpp:387:16: note: Shadowed declaration
hisat2-2.2.1/hisat2_inspect.cpp:419:25: note: Shadow variable
hisat2-2.2.1/hisat2_inspect.cpp:205:20: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat2_inspect.cpp:580:11: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat2_inspect.cpp:508:34: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat2_inspect.cpp:434:33: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat2_inspect.cpp:350:33: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat2_inspect.cpp:335:70: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/word_io.h:374:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.cpp:52:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.cpp:257:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.cpp:324:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.cpp:395:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat2_inspect.cpp:283:18: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/read_qseq.cpp:68:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read_qseq.cpp:119:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read_qseq.cpp:157:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read_qseq.cpp:219:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/ref_read.cpp:204:15: style: Expression is always true because 'else if' condition is opposite to previous condition at line 201. [multiCondition]
hisat2-2.2.1/ref_read.cpp:201:14: note: first condition
hisat2-2.2.1/ref_read.cpp:204:15: note: else if condition is opposite to first condition
hisat2-2.2.1/ref_read.cpp:416:10: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/ref_read.cpp:415:10: note: First condition
hisat2-2.2.1/ref_read.cpp:416:10: note: Second condition
hisat2-2.2.1/ref_read.cpp:376:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:377:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:449:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:450:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/reference.cpp:56:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.cpp:399:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.cpp:442:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.cpp:510:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.cpp:669:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:662:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:691:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HISAT_VERSION [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:864:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:924:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:957:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:1499:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2603:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2691:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2709:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2727:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2746:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:2904:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:3339:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/hisat_bp.cpp:3401:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bp_aligner.h:160:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/bp_aligner.h:245:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/read_qseq.cpp:156:10: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/read_qseq.cpp:148:6: note: Shadowed declaration
hisat2-2.2.1/read_qseq.cpp:156:10: note: Shadow variable
hisat2-2.2.1/scoring.cpp:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/scoring.cpp:107:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/reference.cpp:217:5: warning: Class 'BitPairReference' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/reference.cpp:217:5: warning: Class 'BitPairReference' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/reference.cpp:475:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/reference.cpp:470:12: note: Assuming that condition 'count==0' is not redundant
hisat2-2.2.1/reference.cpp:475:14: note: Condition 'count>0' is always true
hisat2-2.2.1/reference.cpp:639:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/reference.cpp:633:12: note: Assuming that condition 'count==0' is not redundant
hisat2-2.2.1/reference.cpp:639:14: note: Condition 'count>0' is always true
hisat2-2.2.1/reference.cpp:66:3: error: Resource leak: f3 [resourceLeak]
hisat2-2.2.1/reference.cpp:108:4: error: Resource leak: f4 [resourceLeak]
hisat2-2.2.1/reference.cpp:119:3: error: Resource leak: f4 [resourceLeak]
hisat2-2.2.1/reference.cpp:370:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/reference.cpp:439:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/reference.cpp:496:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/reference.cpp:504:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/reference.cpp:576:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/reference.cpp:254:39: style: The scope of the variable 'four_buf2' can be reduced. [variableScope]
hisat2-2.2.1/reference.cpp:500:6: style: The scope of the variable 'off2' can be reduced. [variableScope]
hisat2-2.2.1/reference.cpp:231:10: style: Local variable 'f4' shadows outer variable [shadowVariable]
hisat2-2.2.1/reference.cpp:54:13: note: Shadowed declaration
hisat2-2.2.1/reference.cpp:231:10: note: Shadow variable
hisat2-2.2.1/reference.cpp:341:31: style: Local variable 'tmp_destU32_' shadows outer variable [shadowVariable]
hisat2-2.2.1/reference.h:188:2: note: Shadowed declaration
hisat2-2.2.1/reference.cpp:341:31: note: Shadow variable
hisat2-2.2.1/reference.cpp:219:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/reference.cpp:54:13: style: Variable 'f4' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/reference.cpp:499:11: style: Variable 'dest_2' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/reference.cpp:254:49: style: Variable 'four_buf2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/reference.cpp:289:29: style: Variable 'seq_pos' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/reference.cpp:519:17: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/scoring.cpp:107:2: style: Unsigned expression 'rd.length()' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/scoring.cpp:33:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:33:10: note: Shadow variable
hisat2-2.2.1/scoring.cpp:48:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:48:10: note: Shadow variable
hisat2-2.2.1/scoring.cpp:79:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:79:10: note: Shadow variable
hisat2-2.2.1/simple_func.cpp:36:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:58:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:112:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:635:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:650:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:666:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:690:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:835:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:853:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:868:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:910:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:936:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:951:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:994:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:1012:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:1046:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:1083:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site_new.cpp:1143:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:58:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:119:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:147:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:162:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:178:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:202:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:356:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:374:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:389:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:418:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:446:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:480:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:514:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:533:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:548:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:597:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:616:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:657:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:730:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:778:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/splice_site.cpp:836:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:56:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:104:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:127:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:156:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:228:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:268:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:284:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:295:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:312:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:330:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:508:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:529:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:556:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:624:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:728:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:800:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:948:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:977:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1090:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1214:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1242:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1259:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1324:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1440:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1496:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1671:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:1877:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2101:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2134:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2177:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2196:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2264:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2540:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2594:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:2990:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3117:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3732:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3794:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3816:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3849:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4251:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4273:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4354:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4376:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4390:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4426:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4718:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3202:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3303:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3610:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3642:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3698:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3875:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:3991:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4026:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4088:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4154:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable aligned [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/repeat_builder.cpp:4186:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable snps [valueFlowBailoutIncompleteVar]
hisat2-2.2.1/gfm.h:4990:5: error: Using 'memcpy' on class that contains a virtual function. [memsetClass]
hisat2-2.2.1/ds.h:529:3: error: Using 'memset' on class that contains a 'std::pair'. [memsetClass]
hisat2-2.2.1/ds.h:536:3: error: Using 'memset' on class that contains a 'std::pair'. [memsetClass]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::type' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::pos' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::id' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::repeat_id_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::parent_id_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::self_repeat_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::sa_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::seed_len_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::seed_count_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < SString < char > >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < SString < char > >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < SString < char > >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < SString < char > >::reversed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom'
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange'
hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange'
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < SString < char > >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < SString < char > >::get_alt_range'
hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < SString < char > >::get_alt_range'
hisat2-2.2.1/repeat_builder.h:65:7: style:inconclusive: Technically the member function 'Fragments::contain' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < SString < char > >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < SString < char > >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < SString < char > >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < SString < char > >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < SString < char > >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < SString < char > >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < SString < char > >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < SString < char > >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < SString < char > >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < SString < char > >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Fragments , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Fragments , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Fragments , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SeedSNP * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SeedSNP * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SeedSNP * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < uint32_t , int > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < uint32_t , int > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < uint32_t , int > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < SeedExt , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < SeedExt , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < SeedExt , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < RB_AlleleCoord , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < RB_AlleleCoord , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < RB_AlleleCoord , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < unsigned long , unsigned long > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < unsigned long , unsigned long > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < unsigned long , unsigned long > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < uint32_t , uint32_t > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < uint32_t , uint32_t > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < uint32_t , uint32_t > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint8_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint8_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/repeat_builder.h:649:10: warning: The class 'RB_RepeatExt' defines member function with name 'extendConsensus' also defined in its parent class 'RB_Repeat'. [duplInheritedMember]
hisat2-2.2.1/repeat_builder.h:540:10: note: Parent function 'RB_Repeat::extendConsensus'
hisat2-2.2.1/repeat_builder.h:649:10: note: Derived function 'RB_RepeatExt::extendConsensus'
hisat2-2.2.1/repeat_builder.h:666:10: warning: The class 'RB_RepeatExt' defines member function with name 'get_consensus_seq' also defined in its parent class 'RB_Repeat'. [duplInheritedMember]
hisat2-2.2.1/repeat_builder.h:609:10: note: Parent function 'RB_Repeat::get_consensus_seq'
hisat2-2.2.1/repeat_builder.h:666:10: note: Derived function 'RB_RepeatExt::get_consensus_seq'
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < uint8_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/gfm.h:2435:13: performance: Function 'nPat()' should return member '_nPat' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:2436:13: performance: Function 'nFrag()' should return member '_nFrag' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:187:10: performance: Function 'len()' should return member '_len' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:188:10: performance: Function 'lenNucs()' should return member '_len' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:189:13: performance: Function 'gbwtLen()' should return member '_gbwtLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:190:10: performance: Function 'sz()' should return member '_sz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:191:10: performance: Function 'gbwtSz()' should return member '_gbwtSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:195:10: performance: Function 'offMask()' should return member '_offMask' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:197:10: performance: Function 'eftabLen()' should return member '_eftabLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:198:10: performance: Function 'eftabSz()' should return member '_eftabSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:199:10: performance: Function 'ftabLen()' should return member '_ftabLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:200:10: performance: Function 'ftabSz()' should return member '_ftabSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:201:10: performance: Function 'offsLen()' should return member '_offsLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:202:10: performance: Function 'offsSz()' should return member '_offsSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:203:10: performance: Function 'lineSz()' should return member '_lineSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:204:10: performance: Function 'sideSz()' should return member '_sideSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:205:10: performance: Function 'sideGbtSz()' should return member '_sideGbwtSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:206:10: performance: Function 'sideGbwtLen()' should return member '_sideGbwtLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:207:10: performance: Function 'numSides()' should return member '_numSides' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:208:10: performance: Function 'numLines()' should return member '_numLines' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:209:10: performance: Function 'gbwtTotLen()' should return member '_gbwtTotLen' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:210:10: performance: Function 'gbwtTotSz()' should return member '_gbwtTotSz' by const reference. [returnByReference]
hisat2-2.2.1/gfm.h:213:13: performance: Function 'numNodes()' should return member '_numNodes' by const reference. [returnByReference]
hisat2-2.2.1/gbwt_graph.h:1511:17: performance: Function 'value()' should return member 'to' by const reference. [returnByReference]
hisat2-2.2.1/gbwt_graph.h:121:20: performance: Function 'EdgeTo()' should return member 'to' by const reference. [returnByReference]
hisat2-2.2.1/hisat2_repeat.cpp:819:13: style: Condition 'optind>=argc' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2_repeat.cpp:812:13: note: Assuming that condition 'optind>=argc' is not redundant
hisat2-2.2.1/hisat2_repeat.cpp:819:13: note: Condition 'optind>=argc' is always false
hisat2-2.2.1/hisat2_repeat.cpp:862:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4010:17: style:inconclusive: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:3975:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4010:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:4083:17: style:inconclusive: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:4049:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4083:17: note: bot is overwritten
hisat2-2.2.1/hisat2_repeat.cpp:290:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2_repeat.cpp:779:12: style: The scope of the variable 'outfile' can be reduced. [variableScope]
hisat2-2.2.1/diff_sample.h:479:26: warning: Either the condition 'dcv==0' is redundant or there is division by zero at line 479. [zerodivcond]
hisat2-2.2.1/hisat2_repeat.cpp:653:24: note: Assuming that condition 'dcv==0' is not redundant
hisat2-2.2.1/hisat2_repeat.cpp:663:21: note: Compound assignment '<<=', assigned value is 0
hisat2-2.2.1/hisat2_repeat.cpp:664:101: note: Calling function 'simulateAllocs', 2nd argument 'dcv>>1' value is 0
hisat2-2.2.1/diff_sample.h:479:26: note: Division by zero
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gfm.h:4367:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4367:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4370:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4370:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6479:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6479:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6482:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6482:13: note: Shadow variable
hisat2-2.2.1/gfm.h:5975:14: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5975:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5984:14: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5984:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:1775:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:75:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:1775:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:372:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:75:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:372:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.h:158:56: performance: Function parameter 'bs' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:940:12: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2432:29: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2433:37: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2434:35: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2571:11: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2598:25: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2620:11: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2621:11: performance: Function parameter 'ftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2622:11: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2623:11: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2638:25: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2651:49: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2658:49: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2672:11: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2699:11: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2700:11: performance: Function parameter 'ftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2701:11: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2702:11: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2719:28: performance: Function parameter 'elt' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2743:11: performance: Function parameter 'hitlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3485:11: performance: Function parameter 'top' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3486:11: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3547:11: performance: Function parameter 'num' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3550:11: performance: Function parameter 'maskOff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3625:26: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3639:11: performance: Function parameter 'num' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3763:50: performance: Function parameter 'k' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3893:11: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3958:51: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4174:40: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4495:33: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4565:10: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5528:44: performance: Function parameter 'qlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5529:44: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5604:45: performance: Function parameter 'tid' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5605:45: performance: Function parameter 'textoff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5724:41: performance: Function parameter 'elt' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5726:41: performance: Function parameter 'hitlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:339:20: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:348:11: performance: Function parameter 'top' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:349:11: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:377:30: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:400:44: performance: Function parameter 'top' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:401:44: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:429:34: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:121:11: performance: Function parameter 'len' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:122:17: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:123:17: performance: Function parameter 'numNodes' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:127:17: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:139:23: performance: Function parameter 'len' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:140:23: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:141:23: performance: Function parameter 'numNodes' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:145:23: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1727:55: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1731:52: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1741:53: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:69:35: performance: Function parameter 'value_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:101:37: performance: Function parameter 'to_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:202:83: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:205:81: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:305:44: performance: Function parameter 'node_id' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:329:46: performance: Function parameter 'to_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:348:34: performance: Function parameter 'a' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:348:45: performance: Function parameter 'b' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:815:87: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:359:30: performance: Function parameter 'repID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:359:59: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:373:42: performance: Function parameter 'repID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:375:42: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:379:28: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:430:43: performance: Function parameter 'anchor_left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:431:43: performance: Function parameter 'anchor_right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:432:43: performance: Function parameter 'repID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:434:43: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:438:29: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:439:29: performance: Function parameter 'dist' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:500:49: performance: Function parameter 'repID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:502:49: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:504:49: performance: Function parameter 'repID2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:506:49: performance: Function parameter 'right2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:510:35: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:511:35: performance: Function parameter 'dist' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:609:50: performance: Function parameter 'left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:610:50: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:132:29: performance: Function parameter 'repID_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:133:29: performance: Function parameter 'repPos_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:134:29: performance: Function parameter 'repLen_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:66:23: performance: Function parameter 'allelePos_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:67:23: performance: Function parameter 'alleleLen_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:101:29: performance: Function parameter 'left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:101:43: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:50:88: performance: Function parameter 'l_alleleID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/word_io.h:319:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
hisat2-2.2.1/hisat2_repeat.cpp:858:32: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hisat2_repeat.cpp:714:33: style: Variable 'e' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.h:202:51: style: Parameter 'a' can be declared as pointer to const [constParameterReference]
hisat2-2.2.1/repeat_builder.h:202:72: style: Parameter 'b' can be declared as pointer to const [constParameterReference]
hisat2-2.2.1/radix_sort.h:193:16: error: Shifting 32-bit value by 192 bits is undefined behaviour [shiftTooManyBits]
hisat2-2.2.1/radix_sort.h:192:33: note: Assignment 'log_size=sizeof(maxv)*8', assigned value is 192
hisat2-2.2.1/radix_sort.h:193:16: note: Shift
hisat2-2.2.1/gfm.h:4513:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4524:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:755:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:766:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:767:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:769:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:788:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:870:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:910:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:912:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1186:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1276:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1366:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1400:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1402:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1440:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1456:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1577:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1592:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1646:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1684:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1705:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1739:72: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1742:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1771:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1774:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1805:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1818:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1914:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1920:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1940:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1978:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2024:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2050:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2073:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2178:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2383:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2721:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2786:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2858:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2967:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2976:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3027:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3106:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3581:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3799:27: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3817:27: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3900:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3932:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3991:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4036:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4065:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4192:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4195:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4207:19: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4211:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4222:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4468:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4581:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4582:28: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4583:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4599:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4647:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4653:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4662:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4811:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4876:19: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5000:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5006:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5055:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5081:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5097:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5103:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5115:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5254:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5435:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5451:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5468:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5480:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5625:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5640:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5664:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5672:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5685:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5700:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5704:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6024:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6057:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6205:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6291:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6391:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6643:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6658:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6661:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6670:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6672:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6795:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6834:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6852:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6865:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6871:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6900:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6911:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6952:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:455:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1624:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1641:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1716:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1719:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1734:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1736:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1823:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1866:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1876:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1886:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1900:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1901:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1914:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1919:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1959:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1977:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2051:119: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2060:115: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2068:115: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2164:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2171:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2177:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2187:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2191:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2195:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2213:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2230:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2282:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2356:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2392:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2496:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2612:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2626:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2628:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2643:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2671:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2713:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2739:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:155:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:159:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:178:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:183:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:272:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:387:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:421:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:435:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:473:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:486:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:507:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:512:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:526:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:542:56: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:544:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:548:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:554:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:559:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:573:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:633:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:639:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:678:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:679:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:746:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:799:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:806:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:908:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:913:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:948:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:955:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:994:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:995:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1069:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1099:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1137:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1149:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1182:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1184:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1186:72: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1202:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1216:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1226:22: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1227:22: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1230:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1234:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1243:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1247:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1261:56: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1280:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1337:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1401:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1423:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1427:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1455:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1467:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1473:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:209:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:225:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:229:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:233:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:242:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:251:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:255:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:264:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:268:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:279:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:295:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:298:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:323:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:329:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:335:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:338:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:354:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:403:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:467:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:554:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:559:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:146:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:150:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:164:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:169:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/alt.h:233:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/alt.h:245:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/splice_site_new.cpp:1001:20: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site_new.cpp:1001:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/aligner_report.h:30:7: performance:inconclusive: Technically the member function 'Reporter::report' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_cache.h:898:33: style:inconclusive: Technically the member function 'AlignmentCacheIface < uint32_t >::current' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:290:7: style:inconclusive: Technically the member function 'SAVal < uint32_t >::valid' can be const. [functionConst]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < Pool * , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < Pool * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < Pool * , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < int64_t , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < int64_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < int64_t , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < QKey , QVal < uint32_t > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < QKey , SAVal < uint32_t > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < QKey , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < uint32_t , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sse_util.cpp:27:20: performance:inconclusive: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sse_util.h:510:7: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sse_util.cpp:27:20: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint16_t , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint16_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint16_t , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sse_util.cpp:28:11: style: Parameter 'pvH' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/sse_util.cpp:29:11: style: Parameter 'pvE' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/sse_util.cpp:30:11: style: Parameter 'pvF' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/tinythread.cpp:164:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/tinythread.cpp:224:70: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/tinythread.cpp:135:28: style: The scope of the variable 'idCount' can be reduced. [variableScope]
hisat2-2.2.1/tinythread.cpp:139:30: performance: Searching before insertion is not necessary. Instead of 'idMap[aHandle]=idCount++' consider using 'idMap.try_emplace(aHandle, idCount++);'. [stlFindInsert]
hisat2-2.2.1/tinythread.cpp:222:9: style: Variable 'err' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site_new.cpp:1086:20: style: Checking if unsigned expression 'pool.size()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/splice_site_new.cpp:1043:44: style:inconclusive: Function 'read' argument 2 names different: declaration 'known' definition 'novel'. [funcArgNamesDifferent]
hisat2-2.2.1/splice_site.h:557:34: note: Function 'read' argument 2 names different: declaration 'known' definition 'novel'.
hisat2-2.2.1/splice_site_new.cpp:1043:44: note: Function 'read' argument 2 names different: declaration 'known' definition 'novel'.
hisat2-2.2.1/splice_site_new.cpp:656:23: style: Local variable 'pool' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:581:11: note: Shadowed declaration
hisat2-2.2.1/splice_site_new.cpp:656:23: note: Shadow variable
hisat2-2.2.1/splice_site_new.cpp:656:23: style: Variable 'pool' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/splice_site_new.cpp:697:48: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site_new.cpp:761:36: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site.cpp:605:20: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site.cpp:605:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site.cpp:717:52: style: Condition 'fw=='+'' is always false [knownConditionTrueFalse]
hisat2-2.2.1/splice_site.cpp:663:22: note: Assignment 'fw=alt.fw', assigned value is less than 2
hisat2-2.2.1/splice_site.cpp:717:52: note: Condition 'fw=='+'' is always false
hisat2-2.2.1/splice_site.cpp:781:20: style: Checking if unsigned expression 'pool.size()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/splice_site.cpp:168:23: style: Local variable 'pool' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:581:11: note: Shadowed declaration
hisat2-2.2.1/splice_site.cpp:168:23: note: Shadow variable
hisat2-2.2.1/splice_site.cpp:520:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/splice_site.cpp:517:10: note: Shadowed declaration
hisat2-2.2.1/splice_site.cpp:520:21: note: Shadow variable
hisat2-2.2.1/splice_site.cpp:168:23: style: Variable 'pool' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/splice_site.cpp:216:48: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site.cpp:282:36: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:365:14: warning: Member variable 'CoordHelper::cached_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.cpp:2856:15: warning: Member variable 'RB_SWAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.cpp:172:2: warning: Member variable 'RepeatRange::rg_id' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:940:10: style:inconclusive: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list. [initializerList]
hisat2-2.2.1/repeat_builder.cpp:3174:1: note: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list.
hisat2-2.2.1/repeat_builder.h:940:10: note: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list.
hisat2-2.2.1/repeat_builder.h:250:10: style:inconclusive: Technically the member function 'SeedExt::getLeftExtString' can be const. [functionConst]
hisat2-2.2.1/repeat_builder.h:257:10: style:inconclusive: Technically the member function 'SeedExt::getRightExtString' can be const. [functionConst]
hisat2-2.2.1/repeat_builder.cpp:1484:17: performance:inconclusive: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.h:609:10: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:1484:17: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:1659:20: performance:inconclusive: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.h:666:10: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:1659:20: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:2523:20: performance:inconclusive: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.h:693:10: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:2523:20: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:2906:20: performance:inconclusive: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.h:739:10: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:2906:20: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:3685:27: performance:inconclusive: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.h:922:10: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:3685:27: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:1860:20: warning: The class 'RB_RepeatExt' defines member function with name 'extendConsensus' also defined in its parent class 'RB_Repeat'. [duplInheritedMember]
hisat2-2.2.1/repeat_builder.cpp:784:17: note: Parent function 'RB_Repeat::extendConsensus'
hisat2-2.2.1/repeat_builder.cpp:1860:20: note: Derived function 'RB_RepeatExt::extendConsensus'
hisat2-2.2.1/repeat_builder.cpp:1659:20: warning: The class 'RB_RepeatExt' defines member function with name 'get_consensus_seq' also defined in its parent class 'RB_Repeat'. [duplInheritedMember]
hisat2-2.2.1/repeat_builder.cpp:1484:17: note: Parent function 'RB_Repeat::get_consensus_seq'
hisat2-2.2.1/repeat_builder.cpp:1659:20: note: Derived function 'RB_RepeatExt::get_consensus_seq'
hisat2-2.2.1/repeat_builder.cpp:1528:29: style: Condition 'min_left_ext>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/repeat_builder.cpp:1517:24: note: Assuming that condition 'min_left_ext>0' is not redundant
hisat2-2.2.1/repeat_builder.cpp:1523:69: note: Assuming condition is false
hisat2-2.2.1/repeat_builder.cpp:1528:29: note: Condition 'min_left_ext>0' is always true
hisat2-2.2.1/repeat_builder.cpp:4695:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4701:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4707:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4730:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4739:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4746:9: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/repeat_builder.cpp:4688:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4689:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4690:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4693:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4699:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4705:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4717:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4720:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4723:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4727:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4736:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:4743:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/repeat_builder.cpp:429:10: style: Redundant initialization for 'frag'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/repeat_builder.cpp:417:21: note: frag is initialized
hisat2-2.2.1/repeat_builder.cpp:429:10: note: frag is overwritten
hisat2-2.2.1/repeat_builder.cpp:853:26: style: The scope of the variable 'seed' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3065:13: style: The scope of the variable 'max_match_len' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3351:16: style: The scope of the variable 'query2' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3351:24: style: The scope of the variable 'rc_query2' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:826:23: style: Checking if unsigned expression 'extlen' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1002:21: style: Checking if unsigned expression 'remove_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1346:18: style: Checking if unsigned expression 'max_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1899:23: style: Checking if unsigned expression 'extlen' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:2845:25: style: Checking if unsigned expression 'remove_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:399:47: style:inconclusive: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:88:38: note: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:399:47: note: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:447:44: style:inconclusive: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:89:35: note: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:447:44: note: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:1053:46: style:inconclusive: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:553:39: note: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'.
hisat2-2.2.1/repeat_builder.cpp:1053:46: note: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'.
hisat2-2.2.1/repeat_builder.cpp:3591:63: style:inconclusive: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:926:46: note: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'.
hisat2-2.2.1/repeat_builder.cpp:3591:63: note: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'.
hisat2-2.2.1/repeat_builder.cpp:3949:60: style:inconclusive: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:880:43: note: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'.
hisat2-2.2.1/repeat_builder.cpp:3949:60: note: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'.
hisat2-2.2.1/repeat_builder.cpp:747:24: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:736:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:747:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:1060:36: style: Local variable 'reset' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.h:582:10: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:1060:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2122:21: style: Local variable 'seeds' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.h:523:21: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2122:21: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2370:17: style: Local variable 'left' shadows outer argument [shadowArgument]
hisat2-2.2.1/repeat_builder.cpp:2234:33: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2370:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2370:36: style: Local variable 'right' shadows outer argument [shadowArgument]
hisat2-2.2.1/repeat_builder.cpp:2235:33: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2370:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2436:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2436:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2455:17: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2455:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2468:17: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2468:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3758:36: style: Local variable 'overlap' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3739:22: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3758:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4465:24: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4445:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4469:24: style: Local variable 'saBegin' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4455:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4469:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4499:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4499:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4500:28: style: Local variable 'num' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4446:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4500:28: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4548:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4548:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4558:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4558:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4559:32: style: Local variable 'num' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4446:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4559:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3472:20: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3472:20: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3495:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3495:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3520:20: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3520:20: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:50:22: style: Local variable 'next_kmer' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.cpp:1222:8: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:50:22: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:74:22: style: Local variable 'next_kmer' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.cpp:1222:8: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:74:22: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:142:35: style: Parameter 'coordHelper' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/repeat_builder.cpp:387:17: style: Variable 'nameline' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:600:65: style: Parameter 'snp' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/repeat_builder.cpp:932:29: style: Variable 'range2' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:2030:29: style: Variable 'range2' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:2099:39: style: Parameter 'coordHelper' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/repeat_builder.cpp:3455:20: style: Variable 'repeat' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:3555:34: style: Variable 'seed' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:3565:34: style: Variable 'seed' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/repeat_builder.cpp:3949:60: style: Parameter 'repeat_manager' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/repeat_builder.cpp:3951:51: style: Parameter 'fp' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/repeat_builder.cpp:352:22: style: Parameter 'array' can be declared as const array [constParameter]
hisat2-2.2.1/repeat_builder.cpp:456:16: style: Variable 'frag' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/repeat_builder.h:202:51: style: Parameter 'a' can be declared as pointer to const. However it seems that 'cmpSeedSNPByPos' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/repeat_builder.cpp:2138:52: note: You might need to cast the function pointer here
hisat2-2.2.1/repeat_builder.h:202:51: note: Parameter 'a' can be declared as pointer to const
hisat2-2.2.1/repeat_builder.h:202:72: style: Parameter 'b' can be declared as pointer to const. However it seems that 'cmpSeedSNPByPos' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/repeat_builder.cpp:2138:52: note: You might need to cast the function pointer here
hisat2-2.2.1/repeat_builder.h:202:72: note: Parameter 'b' can be declared as pointer to const
hisat2-2.2.1/repeat_builder.cpp:3802:49: performance: Searching before insertion is not necessary. Instead of 'range_to_repeats_[range]=EList < unsigned long , 128 >()' consider using 'range_to_repeats_.try_emplace(range, EList < unsigned long , 128 >());'. [stlFindInsert]
hisat2-2.2.1/repeat_builder.cpp:2458:25: warning: Either the condition '(offsets[i+1])>=0' is redundant, otherwise there is negative array index -2. [negativeContainerIndex]
hisat2-2.2.1/repeat_builder.cpp:2456:13: note: Assuming that condition '(offsets[i+1])>=0' is not redundant
hisat2-2.2.1/repeat_builder.cpp:2458:25: note: Negative array index
hisat2-2.2.1/repeat_builder.cpp:665:27: style: Variable 'gap_str' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:677:27: style: Variable 'gap_str' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3065:27: style: Variable 'max_match_len' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3088:27: style: Variable 'max_match_len' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3131:17: style: Variable 'ref2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3132:18: style: Variable 'read2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3747:88: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3756:40: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3761:44: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3726:106: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3839:40: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3842:61: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3843:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3184:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3294:104: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3454:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3469:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3496:98: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3550:102: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4034:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4058:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4101:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/hi_aligner.h:5028:20: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5027:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5028:20: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5224:20: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5223:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5224:20: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5507:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5506:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5507:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6081:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6080:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6081:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6317:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6316:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6317:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6903:62: warning: Either the condition 'rdi<2' is redundant or the array '_hits_searched[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6902:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6903:62: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6920:62: warning: Either the condition 'rdi<2' is redundant or the array '_hits_searched[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6918:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6920:62: note: Array index out of bounds
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldS' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newS' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hisat_bp.cpp:1741:2: warning: Member variable 'PerfMetrics::lastElapsed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rds' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_paired' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rightendonly' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_nofw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_norc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minsc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_maxpen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::max_localindexatts' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rds' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_paired' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rightendonly' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_nofw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_norc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minsc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_maxpen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_anchorStop' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minK' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minK_local' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::max_localindexatts' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_thread_rids_mindist' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:432:2: warning: Member variable 'GenomeHit < uint32_t >::_splicescore' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning:inconclusive: Member variable 'GenomeHit < uint32_t >::_fw' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_rdoff' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_len' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_trim5' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_trim3' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_tidx' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_toff' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_joinedOff' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning:inconclusive: Member variable 'GenomeHit < uint32_t >::_repeat' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_score' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_localscore' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:453:5: warning: Member variable 'GenomeHit < uint32_t >::_splicescore' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:478:25: warning:inconclusive: Member variable 'GenomeHit < uint32_t >::_fw' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_rdoff' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_len' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_trim5' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_trim3' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_tidx' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_toff' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_joinedOff' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning:inconclusive: Member variable 'GenomeHit < uint32_t >::_repeat' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_edits' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_ht_list' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_score' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_localscore' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_splicescore' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_hitcount' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_edits_node' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_ht_list_node' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:478:25: warning: Member variable 'GenomeHit < uint32_t >::_sharedVars' is not assigned a value in 'GenomeHit < uint32_t >::operator='. [operatorEqVarError]
hisat2-2.2.1/hi_aligner.h:218:2: warning: Member variable 'ReadBWTHit < uint32_t >::_cur_local' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::node_top' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::node_bot' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::node_top' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::node_bot' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aln_sink.h:669:11: warning: Member variable 'AlnSink < uint32_t >::numWrappers_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:616:2: warning: Member variable 'SeedResults < uint32_t >::sorted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:6282:42: performance:inconclusive: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:5347:10: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/hi_aligner.h:6282:42: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/hi_aligner.h:1192:6: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::mms' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:1204:6: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::ns' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:1218:9: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::ngaps' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:267:13: style:inconclusive: Technically the member function 'ReadBWTHit < uint32_t >::numPartialSearch' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S < uint32_t , EListSlice < uint32_t , 16 > , 16 >::resolveAll' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S < uint16_t , EListSlice < uint16_t , 16 > , 16 >::resolveAll' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit < uint32_t , EListSlice < uint32_t , 16 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit < uint16_t , EListSlice < uint16_t , 16 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:3024:27: style:inconclusive: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const. [functionConst]
hisat2-2.2.1/aln_sink.h:1592:7: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
hisat2-2.2.1/aln_sink.h:3024:27: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
hisat2-2.2.1/aln_sink.h:1220:28: style:inconclusive: Technically the member function 'AlnSinkWrap < uint32_t >::reportingParams' can be const. [functionConst]
hisat2-2.2.1/aln_sink.h:1637:24: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:881:7: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:417:26: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:187:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printOptFieldEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:210:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printOptFieldNewlineEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:469:26: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/ds.h:1227:29: performance:inconclusive: Technically the member function 'ELList < Edit , 128 , 4 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < pair < int , string > , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < pair < int , string > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < pair < int , string > , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint64_t , 128 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint64_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint64_t , 128 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/aligner_sw_driver.h:194:2: style: Class 'RowSampler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_sw_driver.h:312:2: style: Class 'SwDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/hi_aligner.h:3970:2: style: Class 'HI_Aligner < uint32_t , uint16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState < uint16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aln_sink.h:1539:11: style: The destructor '~AlnSinkSam < uint32_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aln_sink.h:687:11: note: Virtual destructor in base class
hisat2-2.2.1/aln_sink.h:1539:11: note: Destructor in derived class
hisat2-2.2.1/hisat_bp.cpp:1412:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat_bp.cpp:1451:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/group_walk.h:681:3: style: Comparing expression of type 'unsigned short' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/aligner_metrics.h:201:27: style: Condition 'ent<0.75f' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
hisat2-2.2.1/aligner_metrics.h:201:27: note: Condition 'ent<0.75f' is always true
hisat2-2.2.1/aligner_metrics.h:202:25: style: Condition 'ent<0.001f' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
hisat2-2.2.1/aligner_metrics.h:202:25: note: Condition 'ent<0.001f' is always true
hisat2-2.2.1/aligner_sw_driver.h:1042:46: style: Condition 'keepWhole' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_sw_driver.h:1041:19: note: Assignment 'keepWhole=false', assigned value is 0
hisat2-2.2.1/aligner_sw_driver.h:1042:46: note: Condition 'keepWhole' is always false
hisat2-2.2.1/hisat_bp.cpp:1395:19: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:1390:38: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat_bp.cpp:1395:19: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat_bp.cpp:3242:28: style: Condition '!done[mate]' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:3240:24: note: Assuming that condition '!done[mate]' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3242:28: note: Condition '!done[mate]' is always true
hisat2-2.2.1/hi_aligner.h:5987:40: style: Condition 'r2.repeat()' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hi_aligner.h:5987:25: note: Assuming that condition 'r1.repeat()' is not redundant
hisat2-2.2.1/hi_aligner.h:5983:28: note: Assuming that condition 'r1.repeat()!=r2.repeat()' is not redundant
hisat2-2.2.1/hi_aligner.h:5987:40: note: Condition 'r2.repeat()' is always true
hisat2-2.2.1/hi_aligner.h:2218:8: style: Condition 'doLeftAlign' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hi_aligner.h:2056:24: note: Assignment 'doLeftAlign=false', assigned value is 0
hisat2-2.2.1/hi_aligner.h:2218:8: note: Condition 'doLeftAlign' is always false
hisat2-2.2.1/aligner_sw_driver.h:1316:13: warning: Either the condition 'msink!=NULL' is redundant or there is possible null pointer dereference: msink. [nullPointerRedundantCheck]
hisat2-2.2.1/aligner_sw_driver.h:1319:37: note: Assuming that condition 'msink!=NULL' is not redundant
hisat2-2.2.1/aligner_sw_driver.h:1316:13: note: Null pointer dereference
hisat2-2.2.1/hisat_bp.cpp:3525:4: warning: Either the condition 'fout!=NULL' is redundant or there is possible null pointer dereference: fout. [nullPointerRedundantCheck]
hisat2-2.2.1/hisat_bp.cpp:3736:11: note: Assuming that condition 'fout!=NULL' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3525:4: note: Null pointer dereference
hisat2-2.2.1/hisat_bp.cpp:3696:5: warning: Either the condition 'ebwtBw!=NULL' is redundant or there is possible null pointer dereference: ebwtBw. [nullPointerRedundantCheck]
hisat2-2.2.1/hisat_bp.cpp:3704:13: note: Assuming that condition 'ebwtBw!=NULL' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3696:5: note: Null pointer dereference
hisat2-2.2.1/hisat_bp.cpp:2815:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat_bp.cpp:3377:78: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/bp_aligner.h:347:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/bp_aligner.h:818:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4157:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4159:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4161:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4163:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4288:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:4289:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:5618:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hi_aligner.h:5929:54: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hisat_bp.cpp:3221:64: style: The comparison 'mate == 0' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:3212:35: note: 'mate' is assigned value '0' here.
hisat2-2.2.1/hisat_bp.cpp:3221:64: note: The comparison 'mate == 0' is always true.
hisat2-2.2.1/aligner_sw_driver.h:2475:8: style: Variable 'ominsc_cur' is assigned an expression that holds the same value. [redundantAssignment]
hisat2-2.2.1/aligner_sw_driver.h:2468:27: note: ominsc_cur is assigned 'ominsc' here.
hisat2-2.2.1/aligner_sw_driver.h:2475:8: note: Variable 'ominsc_cur' is assigned an expression that holds the same value.
hisat2-2.2.1/hisat_bp.cpp:873:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat_bp.cpp:995:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/aligner_sw_driver.h:1160:9: style: The scope of the variable 'nlarge_elts' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:1625:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2323:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2453:11: style: The scope of the variable 'foundMate' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2670:8: style: The scope of the variable 'refid' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2671:16: style: The scope of the variable 'off1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2671:22: style: The scope of the variable 'off2' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2672:15: style: The scope of the variable 'len1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2672:21: style: The scope of the variable 'len2' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2673:13: style: The scope of the variable 'fw1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2673:18: style: The scope of the variable 'fw2' can be reduced. [variableScope]
hisat2-2.2.1/hisat_bp.cpp:3201:22: style: The scope of the variable 'done' can be reduced. [variableScope]
hisat2-2.2.1/bp_aligner.h:846:18: style: The scope of the variable 'uniqueStop' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:5843:37: style: The scope of the variable 'global_tidx' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1247:23: style: The scope of the variable 'next_i' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1402:13: style: The scope of the variable 'refdif' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1403:13: style: The scope of the variable 'rddif' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1553:21: style: The scope of the variable 'temp_scores' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1554:21: style: The scope of the variable 'temp_scores2' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1570:11: style: The scope of the variable 'maxsplscore' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:2150:17: style: The scope of the variable 'rr' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:573:21: style: Unsigned expression '_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:956:9: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1014:9: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1393:5: style: Unsigned expression 'this_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1396:5: style: Unsigned expression 'other_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1452:5: style: Unsigned expression 'this_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1461:5: style: Unsigned expression 'other_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:2940:9: style: Unsigned expression 'rdoff' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/group_walk.h:681:3: style: Unsigned expression 'trimBegin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw_driver.h:596:18: style:inconclusive: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:466:17: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
hisat2-2.2.1/aligner_sw_driver.h:596:18: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
hisat2-2.2.1/aligner_sw_driver.h:1014:24: style:inconclusive: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:485:15: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
hisat2-2.2.1/aligner_sw_driver.h:1014:24: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
hisat2-2.2.1/aligner_sw_driver.h:1312:34: style:inconclusive: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:366:25: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
hisat2-2.2.1/aligner_sw_driver.h:1312:34: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
hisat2-2.2.1/aligner_sw_driver.h:1923:23: style:inconclusive: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:391:14: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
hisat2-2.2.1/aligner_sw_driver.h:1923:23: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
hisat2-2.2.1/aligner_sw_driver.h:1950:42: style:inconclusive: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:418:33: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
hisat2-2.2.1/aligner_sw_driver.h:1950:42: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:649:29: style: Local variable 'rn' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:627:11: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:649:29: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:671:29: style: Local variable 'width' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:643:25: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:671:29: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:687:33: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:669:25: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:687:33: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:760:21: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:727:15: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:760:21: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:762:25: style: Local variable 'width' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:734:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:762:25: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:777:28: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:760:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:777:28: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:870:22: style: Local variable 'tloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:838:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:870:22: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:870:28: style: Local variable 'bloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:838:27: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:870:28: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:1228:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:3389:15: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:1228:11: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:1240:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:3389:15: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:1240:11: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:3201:22: style: Local variable 'done' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:2944:25: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:3201:22: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:559:29: style: Local variable 'minsc' shadows outer variable [shadowVariable]
hisat2-2.2.1/bp_aligner.h:554:21: note: Shadowed declaration
hisat2-2.2.1/bp_aligner.h:559:29: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:1034:29: style: Local variable 'minsc' shadows outer variable [shadowVariable]
hisat2-2.2.1/bp_aligner.h:1029:21: note: Shadowed declaration
hisat2-2.2.1/bp_aligner.h:1034:29: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4106:30: style: Local variable 'fw' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4072:14: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4106:30: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4246:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4246:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4249:26: style: Local variable 'fw' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4072:14: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4249:26: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4255:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4255:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4293:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4293:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4300:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4300:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4357:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4357:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:1470:13: style: Local variable 'len' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:827:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:1470:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:1478:10: style: Local variable 'spliced' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:1086:22: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:1478:10: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3639:13: style: Local variable 'refoff' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:895:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3639:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3722:13: style: Local variable 'score' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:910:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3722:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3723:12: style: Local variable 'splicescore' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:912:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3723:12: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3724:13: style: Local variable 'localscore' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:911:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3724:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:325:21: style: Local variable 'len' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:262:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:325:21: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2685:19: style: Local variable 'queries' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:229:22: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2685:19: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:184:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/bp_aligner.h:185:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/bp_aligner.h:194:29: style: Variable 'genomeHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/bp_aligner.h:558:41: style: Variable 'tempHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/bp_aligner.h:1033:41: style: Variable 'tempHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:4187:46: style: Variable 'partialHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:4199:46: style: Variable 'partialHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:4236:42: style: Variable 'partialHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:4262:42: style: Variable 'partialHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:5036:34: style: Variable 'partialHit_j' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:5045:34: style: Variable 'partialHit_k' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:5957:79: style: Parameter 'wlm' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:5958:79: style: Parameter 'prm' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:5959:79: style: Parameter 'him' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:5960:79: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:6283:77: style: Parameter 'sink' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:6312:85: style: Parameter 'sink' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:6619:84: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:6764:93: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:1255:27: style: Variable 'next_ed' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:1290:43: style: Variable 'ii_ed' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hi_aligner.h:2038:60: style: Parameter 'swa' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:2039:60: style: Parameter 'swm' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:2040:60: style: Parameter 'prm' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hi_aligner.h:2043:60: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/group_walk.h:340:32: style: Parameter 'sa' can be declared as reference to const [constParameterReference]
hisat2-2.2.1/hisat_bp.cpp:3035:12: style: Variable 'rdlens' can be declared as const array [constVariable]
hisat2-2.2.1/hi_aligner.h:528:41: style: Parameter 'edits' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/hi_aligner.h:529:47: style: Parameter 'ht_list' can be declared as pointer to const [constParameterPointer]
hisat2-2.2.1/hi_aligner.h:4019:39: style: Parameter 'nofw' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:53: style: Parameter 'norc' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:71: style: Parameter 'minsc' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:90: style: Parameter 'maxpen' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4174:25: style: Variable 'fwi' can be declared as const array [constVariable]
hisat2-2.2.1/hi_aligner.h:5929:43: style: Variable 'localGFM' can be declared as pointer to const [constVariablePointer]
hisat2-2.2.1/hi_aligner.h:323:40: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
hisat2-2.2.1/hisat2.cpp:3185:34: style:inconclusive: Boolean expression 'sensitive' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/hisat_bp.cpp:2671:20: style: struct member 'PerfMetrics::lastElapsed' is never used. [unusedStructMember]
hisat2-2.2.1/hisat2.cpp:2075:2: warning: Member variable 'PerfMetrics::lastElapsed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM < uint32_t >::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM < uint32_t >::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::_in1' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::_in2' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:693:5: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:694:5: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint32_t , 16 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint32_t , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint32_t , 16 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:527:7: style:inconclusive: Technically the member function 'EList < uint16_t , 16 >::fillZero' can be const. [functionConst]
hisat2-2.2.1/ds.h:724:18: performance:inconclusive: Technically the member function 'EList < uint16_t , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:731:21: performance:inconclusive: Technically the member function 'EList < uint16_t , 16 >::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/rfm.h:494:31: warning: The class 'RFM < uint32_t >' defines member variable with name '_in1' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4261:14: note: Parent variable 'GFM < uint32_t >::_in1'
hisat2-2.2.1/rfm.h:494:31: note: Derived variable 'RFM < uint32_t >::_in1'
hisat2-2.2.1/rfm.h:495:31: warning: The class 'RFM < uint32_t >' defines member variable with name '_in2' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4262:14: note: Parent variable 'GFM < uint32_t >::_in2'
hisat2-2.2.1/rfm.h:495:31: note: Derived variable 'RFM < uint32_t >::_in2'
hisat2-2.2.1/rfm.h:496:30: warning: The class 'RFM < uint32_t >' defines member variable with name '_in1Str' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4263:13: note: Parent variable 'GFM < uint32_t >::_in1Str'
hisat2-2.2.1/rfm.h:496:30: note: Derived variable 'RFM < uint32_t >::_in1Str'
hisat2-2.2.1/rfm.h:497:30: warning: The class 'RFM < uint32_t >' defines member variable with name '_in2Str' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4264:13: note: Parent variable 'GFM < uint32_t >::_in2Str'
hisat2-2.2.1/rfm.h:497:30: note: Derived variable 'RFM < uint32_t >::_in2Str'
hisat2-2.2.1/rfm.h:499:31: warning: The class 'RFM < uint32_t >' defines member variable with name 'mmFile1_' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4291:11: note: Parent variable 'GFM < uint32_t >::mmFile1_'
hisat2-2.2.1/rfm.h:499:31: note: Derived variable 'RFM < uint32_t >::mmFile1_'
hisat2-2.2.1/rfm.h:500:31: warning: The class 'RFM < uint32_t >' defines member variable with name 'mmFile2_' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4292:8: note: Parent variable 'GFM < uint32_t >::mmFile2_'
hisat2-2.2.1/rfm.h:500:31: note: Derived variable 'RFM < uint32_t >::mmFile2_'
hisat2-2.2.1/rfm.h:381:7: warning: The class 'RFM < uint32_t >' defines member function with name 'loadIntoMemory' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:2525:7: note: Parent function 'GFM < uint32_t >::loadIntoMemory'
hisat2-2.2.1/rfm.h:381:7: note: Derived function 'RFM < uint32_t >::loadIntoMemory'
hisat2-2.2.1/rfm.h:416:7: warning: The class 'RFM < uint32_t >' defines member function with name 'evictFromMemory' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:2548:7: note: Parent function 'GFM < uint32_t >::evictFromMemory'
hisat2-2.2.1/rfm.h:416:7: note: Derived function 'RFM < uint32_t >::evictFromMemory'
hisat2-2.2.1/rfm.h:425:7: warning: The class 'RFM < uint32_t >' defines member function with name 'sanityCheckAll' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:6830:20: note: Parent function 'GFM < uint32_t >::sanityCheckAll'
hisat2-2.2.1/rfm.h:425:7: note: Derived function 'RFM < uint32_t >::sanityCheckAll'
hisat2-2.2.1/spliced_aligner.h:55:10: style: The function 'hybridSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/hi_aligner.h:4812:10: note: Virtual function in base class
hisat2-2.2.1/spliced_aligner.h:55:10: note: Function in derived class
hisat2-2.2.1/spliced_aligner.h:81:13: style: The function 'hybridSearch_recur' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/hi_aligner.h:4839:13: note: Virtual function in base class
hisat2-2.2.1/spliced_aligner.h:81:13: note: Function in derived class
hisat2-2.2.1/hisat2.cpp:1601:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1644:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1663:32: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1557:19: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:1552:38: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat2.cpp:1557:19: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat2.cpp:1575:28: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:1570:47: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat2.cpp:1575:28: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat2.cpp:3589:28: style: Condition '!done[mate]' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:3587:24: note: Assuming that condition '!done[mate]' is not redundant
hisat2-2.2.1/hisat2.cpp:3589:28: note: Condition '!done[mate]' is always true
hisat2-2.2.1/aligner_sw_driver.h:1164:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_sw_driver.h:1166:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_sw_driver.h:2453:21: style: Variable 'foundMate' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3149:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2.cpp:3688:76: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/spliced_aligner.h:843:52: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/spliced_aligner.h:1525:52: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
hisat2-2.2.1/hisat_bp.cpp:3130:15: style: Variable 'nceil[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3148:21: style: Variable 'interval[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3158:18: style: Variable 'mtStreak[0]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3158:32: style: Variable 'mtStreak[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3165:22: style: Variable 'mtStreak[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3243:40: style: Variable 'done[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3710:15: style: Variable 'repThresh' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3568:64: style: The comparison 'mate == 0' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:3559:35: note: 'mate' is assigned value '0' here.
hisat2-2.2.1/hisat2.cpp:3568:64: note: The comparison 'mate == 0' is always true.
hisat2-2.2.1/hi_aligner.h:3637:22: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hi_aligner.h:3654:26: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hi_aligner.h:3665:14: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/group_walk.h:1059:13: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/group_walk.h:1276:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/spliced_aligner.h:188:15: style: Redundant initialization for 'maxsc'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/spliced_aligner.h:187:23: note: maxsc is initialized
hisat2-2.2.1/spliced_aligner.h:188:15: note: maxsc is overwritten
hisat2-2.2.1/hisat2.cpp:1028:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2.cpp:1150:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2.cpp:3527:22: style: The scope of the variable 'done' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:408:18: style: The scope of the variable 'another_spliced' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:1553:18: style: The scope of the variable 'uniqueStop' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:485:42: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:606:46: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:750:38: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:1433:38: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:1387:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3700:15: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:1387:11: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:1399:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3700:15: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:1399:11: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:3527:22: style: Local variable 'done' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3274:25: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:3527:22: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:4083:21: style: Local variable 'gpol' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:2018:42: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:4083:21: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:224:64: style: Local variable 'maxhalf' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:213:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:224:64: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:237:24: style: Local variable 'cminlen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:227:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:237:24: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:237:40: style: Local variable 'cpow2' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:228:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:237:40: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4152:14: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4152:14: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4669:18: style: Local variable 'pseudogeneStop' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:264:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4669:18: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4670:18: style: Local variable 'anchorStop' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:263:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4670:18: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:2059:19: style: Local variable 'minIntronLen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:253:15: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:2059:19: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:2060:19: style: Local variable 'maxIntronLen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:254:15: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:2060:19: note: Shadow variable
hisat2-2.2.1/aln_sink.h:2207:54: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/aln_sink.h:2207:54: note: Shadow variable
hisat2-2.2.1/hgfm.h:2585:10: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2585:10: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:2165:48: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2165:48: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2685:19: style: Local variable 'queries' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:233:22: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2685:19: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:880:13: style: Local variable 'nthreads' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:92:12: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:880:13: note: Shadow variable
hisat2-2.2.1/repeat.h:296:30: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:296:30: note: Shadow variable
hisat2-2.2.1/repeat.h:336:30: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:336:30: note: Shadow variable
hisat2-2.2.1/repeat.h:365:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:365:32: note: Shadow variable
hisat2-2.2.1/repeat.h:387:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:387:32: note: Shadow variable
hisat2-2.2.1/repeat.h:447:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:447:32: note: Shadow variable
hisat2-2.2.1/repeat.h:520:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:520:32: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:175:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/spliced_aligner.h:176:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/spliced_aligner.h:1040:41: style: Variable 'tempHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/spliced_aligner.h:1727:41: style: Variable 'tempHit' can be declared as reference to const [constVariableReference]
hisat2-2.2.1/hisat2.cpp:3361:12: style: Variable 'rdlens' can be declared as const array [constVariable]
hisat2-2.2.1/hisat2.cpp:3962:20: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
hisat2-2.2.1/hisat2.cpp:3969:20: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
hisat2-2.2.1/rfm.h:901:5: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
hisat2-2.2.1/rfm.h:911:5: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
hisat2-2.2.1/hisat2.cpp:3005:20: style: struct member 'PerfMetrics::lastElapsed' is never used. [unusedStructMember]
hisat2-2.2.1/hisat2.cpp:3456:15: style: Variable 'nceil[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3474:21: style: Variable 'interval[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3484:18: style: Variable 'mtStreak[0]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3484:32: style: Variable 'mtStreak[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3491:22: style: Variable 'mtStreak[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3590:40: style: Variable 'done[mate]' is assigned a value that is never used. [unreadVariable]
diff:
2.17.0 hisat2-2.2.1/aligner_bt.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_bt.cpp:704:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_bt.cpp:704:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_bt.cpp:705:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_bt.cpp:705:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_bt.cpp:716:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_bt.cpp:716:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_bt.cpp:717:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_bt.cpp:717:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_driver.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_result.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/aligner_result.cpp:1043:14: performance:inconclusive: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_result.h:1357:8: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_result.cpp:1043:14: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/aligner_result.h:1357:8: performance:inconclusive: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_result.cpp:1043:14: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_result.h:1357:8: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/aligner_seed.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_seed.h:1407:7: performance:inconclusive: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_seed.h:1611:28: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_seed.h:1407:7: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/aligner_seed.h:1611:28: performance:inconclusive: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_seed.h:1407:7: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_seed.h:1611:28: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/aligner_seed2.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_seed2.h:1204:7: performance:inconclusive: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_seed2.h:3354:24: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_seed2.h:1204:7: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/aligner_seed2.h:3354:24: performance:inconclusive: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aligner_seed2.h:1204:7: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aligner_seed2.h:3354:24: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/aligner_seed2.h:687:11: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_seed2.h:687:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_sw.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_sw.cpp:199:8: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_sw.cpp:199:8: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_sw.cpp:332:8: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_sw.cpp:332:8: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_swsse.cpp:83:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse.cpp:83:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse.cpp:86:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse.cpp:86:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse.h:233:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse.h:233:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse.h:236:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse.h:236:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1137:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1137:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1233:29: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1233:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1392:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1392:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1400:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1400:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1405:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1405:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1451:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1451:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1452:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1452:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1453:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1453:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1508:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1508:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1509:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1509:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1510:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1510:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1511:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1511:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1512:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1512:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1513:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1513:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:607:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:607:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:660:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:660:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:661:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:661:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:662:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:662:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:710:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:710:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:711:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:711:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_i16.cpp:712:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_i16.cpp:712:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1122:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1122:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1218:29: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1218:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1377:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1377:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1385:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1385:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1390:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1390:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1436:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1436:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1437:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1437:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1438:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1438:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1493:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1493:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1494:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1494:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1495:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1495:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1496:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1496:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1497:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1497:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1498:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1498:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:599:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:599:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:652:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:652:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:653:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:653:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:654:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:654:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:705:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:705:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_ee_u8.cpp:707:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_ee_u8.cpp:707:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1515:32: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1515:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1554:33: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1554:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1743:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1743:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1751:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1751:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1756:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1756:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1806:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1806:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1807:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1807:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1808:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1808:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1863:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1863:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1864:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1864:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1865:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1865:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1866:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1866:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1867:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1867:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1868:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1868:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:755:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:755:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:756:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:756:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:757:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:757:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:805:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:805:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_i16.cpp:807:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_i16.cpp:807:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1517:31: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1517:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1554:32: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1554:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1747:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1747:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1755:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1755:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1760:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1760:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1806:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1806:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1807:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1807:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1808:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1808:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1863:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1863:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1864:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1864:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1865:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1865:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1866:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1866:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1867:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1867:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1868:41: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1868:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:710:40: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:761:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:761:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:762:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:762:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:763:24: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:763:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:810:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:810:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/aligner_swsse_loc_u8.cpp:812:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:812:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/aligner_swsse_loc_u8.cpp:902:39: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/aln_sink.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/aln_sink.h:1592:7: style:inconclusive: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const. [functionConst]
     hisat2-2.2.1/aln_sink.h:3024:27: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
     hisat2-2.2.1/aln_sink.h:1592:7: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
head hisat2-2.2.1/aln_sink.h:1637:24: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/aln_sink.h:1637:24: performance:inconclusive: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/aln_sink.h:3024:27: style:inconclusive: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const. [functionConst]
     hisat2-2.2.1/aln_sink.h:1592:7: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
     hisat2-2.2.1/aln_sink.h:3024:27: note: Technically the member function 'AlnSinkSam < uint32_t >::appendMate' can be const.
2.17.0 hisat2-2.2.1/aln_sink.h:843:7: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/aln_sink.h:843:7: performance:inconclusive: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < SString < char > >::fw' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < SString < char > >::reversed' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint16_t >::fw' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint16_t >::reversed' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint32_t >::fw' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT < uint32_t >::reversed' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT::fw' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/alt.h:44:5: warning: Member variable 'ALT::reversed' is not initialized in the constructor. [uninitMemberVar]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:101:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:101:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:106:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:106:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:111:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:111:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:115:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:115:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:123:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:123:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/bit_packed_array.cpp:187:22: style:inconclusive: Technically the member function 'BitPackedArray::setItem' can be const. [functionConst]
     hisat2-2.2.1/bit_packed_array.h:76:10: note: Technically the member function 'BitPackedArray::setItem' can be const.
     hisat2-2.2.1/bit_packed_array.cpp:187:22: note: Technically the member function 'BitPackedArray::setItem' can be const.
head hisat2-2.2.1/bit_packed_array.cpp:229:22: style: Unused private function: 'BitPackedArray::expand' [unusedPrivateFunction]
     hisat2-2.2.1/bit_packed_array.h:82:10: note: Unused private function: 'BitPackedArray::expand'
     hisat2-2.2.1/bit_packed_array.cpp:229:22: note: Unused private function: 'BitPackedArray::expand'
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:50:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:50:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:51:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:51:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:52:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:52:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:53:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:53:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:54:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:54:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:56:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:56:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:57:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:57:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:59:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:59:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:63:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:63:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/bit_packed_array.cpp:65:18: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:65:19: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:88:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:88:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:92:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:92:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:95:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:95:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.cpp:98:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bit_packed_array.cpp:98:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bit_packed_array.h:76:10: style:inconclusive: Technically the member function 'BitPackedArray::setItem' can be const. [functionConst]
     hisat2-2.2.1/bit_packed_array.cpp:187:22: note: Technically the member function 'BitPackedArray::setItem' can be const.
     hisat2-2.2.1/bit_packed_array.h:76:10: note: Technically the member function 'BitPackedArray::setItem' can be const.
2.17.0 hisat2-2.2.1/bit_packed_array.h:82:10: style: Unused private function: 'BitPackedArray::expand' [unusedPrivateFunction]
head hisat2-2.2.1/blockwise_sa.h:445:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/blockwise_sa.h:445:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/blockwise_sa.h:445:26: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bp_aligner.h:347:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bp_aligner.h:347:63: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/bp_aligner.h:818:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/bp_aligner.h:818:63: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/ds.h:3406:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/ds.h:3406:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/ds.h:4176:14: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/ds.h:4176:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/edit.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/endian_swap.h:31:11: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/endian_swap.h:31:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/filebuf.h:484:16: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/filebuf.h:484:17: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/filebuf.h:504:15: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/filebuf.h:504:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/filebuf.h:686:14: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/filebuf.h:686:15: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/gbwt_graph.h:1519:27: performance: Function 'PathNodeFrom()' should return member 'from' by const reference. [returnByReference]
2.17.0 hisat2-2.2.1/gbwt_graph.h:1569:27: performance: Function 'PathEdgeTo()' should return member 'to' by const reference. [returnByReference]
2.17.0 hisat2-2.2.1/gbwt_graph.h:1824:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom'
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom'
2.17.0 hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom'
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom'
2.17.0 hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom'
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom'
2.17.0 hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph::findEdgesFrom' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph::findEdgesFrom' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph::findEdgesFrom'
     hisat2-2.2.1/gbwt_graph.h:202:35: note: Unused private function: 'RefGraph::findEdgesFrom'
2.17.0 hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange'
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange'
2.17.0 hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange'
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange'
2.17.0 hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange'
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange'
2.17.0 hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph::getNextEdgeRange' [unusedPrivateFunction]
head hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph::getNextEdgeRange' [unusedPrivateFunction]
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph::getNextEdgeRange'
     hisat2-2.2.1/gbwt_graph.h:208:35: note: Unused private function: 'RefGraph::getNextEdgeRange'
2.17.0 hisat2-2.2.1/gbwt_graph.h:2311:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/gbwt_graph.h:2338:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/gfm.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/gfm.h:2599:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/gfm.h:2639:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable index_t [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/gfm.h:3151:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3210:36: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3210:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3254:36: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3254:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3357:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3357:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3432:38: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3432:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3792:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3792:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3794:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3794:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3813:31: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3813:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3815:31: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3815:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3984:23: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3984:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:3986:23: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:3986:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:4058:23: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:4058:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:4060:23: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:4060:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:4125:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:4125:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/gfm.h:4946:15: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/gfm.h:4946:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:4949:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/gfm.h:4949:57: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:5381:24: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/gfm.h:5381:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:6359:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:6387:50: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:6387:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/gfm.h:6407:38: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/gfm.h:6407:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/gfm.h:6656:20: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/gfm.h:6656:21: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/group_walk.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/hgfm.h:1002:24: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hgfm.h:1002:25: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hgfm.h:1490:29: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hgfm.h:1490:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/hgfm.h:1513:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/hgfm.h:582:15: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hgfm.h:582:16: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hgfm.h:585:63: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4157:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4157:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4159:28: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4159:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4161:32: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4161:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4163:39: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4163:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4288:39: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4288:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:4289:46: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:4289:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:5347:10: performance:inconclusive: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/hi_aligner.h:6282:42: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/hi_aligner.h:5347:10: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/hi_aligner.h:5618:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:5618:49: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hi_aligner.h:5929:54: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hi_aligner.h:5929:54: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/hi_aligner.h:6282:42: performance:inconclusive: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/hi_aligner.h:5347:10: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/hi_aligner.h:6282:42: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/hisat2.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/hisat2_build.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/hisat2_build_main.cpp:54:26: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2_build_main.cpp:54:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2_build_main.cpp:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
     hisat2-2.2.1/hisat2_build_main.cpp:54:46: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2_build_main.cpp:54:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
     hisat2-2.2.1/hisat2_build_main.cpp:56:5: note: Null pointer dereference
2.17.0 hisat2-2.2.1/hisat2_inspect.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/hisat2_inspect.cpp:220:18: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2_inspect.cpp:220:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/hisat2_main.cpp:53:26: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2_main.cpp:53:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2_main.cpp:55:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
     hisat2-2.2.1/hisat2_main.cpp:53:46: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2_main.cpp:53:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
     hisat2-2.2.1/hisat2_main.cpp:55:5: note: Null pointer dereference
2.17.0 hisat2-2.2.1/hisat2_repeat.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/hisat2_repeat_main.cpp:54:26: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2_repeat_main.cpp:54:27: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2_repeat_main.cpp:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
     hisat2-2.2.1/hisat2_repeat_main.cpp:54:46: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2_repeat_main.cpp:54:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
     hisat2-2.2.1/hisat2_repeat_main.cpp:56:5: note: Null pointer dereference
head hisat2-2.2.1/hisat2lib/ht2_index.cpp:33:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_index.cpp:33:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_index.cpp:49:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_index.cpp:49:30: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: note: Null pointer addition
head hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:33: note: Null pointer addition
head hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:51: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:52: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:32: warning: If memory allocation fails, then there is a possible null pointer dereference: result [nullPointerOutOfMemory]
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assuming allocation function fails
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:63:23: note: Assignment 'ptr=malloc(result_hdr_size+result_buf_size)', assigned value is 0
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:49: note: result is assigned '(struct ht2_index_getrefnames_result*)ptr' here.
     hisat2-2.2.1/hisat2lib/ht2_index.cpp:74:32: note: Null pointer dereference
head hisat2-2.2.1/hisat2lib/ht2_init.cpp:184:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_init.cpp:184:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_init.cpp:208:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_init.cpp:208:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:32:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:32:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:58:29: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:58:30: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:47: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:48: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/hisat_bp.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
2.17.0 hisat2-2.2.1/reference.cpp:370:22: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/reference.cpp:370:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/reference.cpp:439:18: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/reference.cpp:439:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/reference.cpp:496:18: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/reference.cpp:496:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/reference.cpp:504:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/reference.cpp:504:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/reference.cpp:576:9: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/reference.cpp:576:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/repeat.h:268:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
2.17.0 hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < SString < char > >::get_alt_range' [unusedPrivateFunction]
head hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < SString < char > >::get_alt_range' [unusedPrivateFunction]
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < SString < char > >::get_alt_range'
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < SString < char > >::get_alt_range'
2.17.0 hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint16_t >::get_alt_range' [unusedPrivateFunction]
head hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint16_t >::get_alt_range' [unusedPrivateFunction]
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint16_t >::get_alt_range'
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint16_t >::get_alt_range'
2.17.0 hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint32_t >::get_alt_range' [unusedPrivateFunction]
head hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint32_t >::get_alt_range' [unusedPrivateFunction]
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint32_t >::get_alt_range'
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB < uint32_t >::get_alt_range'
2.17.0 hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB::get_alt_range' [unusedPrivateFunction]
head hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB::get_alt_range' [unusedPrivateFunction]
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB::get_alt_range'
     hisat2-2.2.1/repeat.h:608:28: note: Unused private function: 'RepeatDB::get_alt_range'
2.17.0 hisat2-2.2.1/repeat_builder.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/repeat_builder.cpp:1484:17: performance:inconclusive: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.h:609:10: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.cpp:1484:17: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/repeat_builder.cpp:1659:20: performance:inconclusive: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.h:666:10: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.cpp:1659:20: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/repeat_builder.cpp:2523:20: performance:inconclusive: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.h:693:10: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.cpp:2523:20: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/repeat_builder.cpp:2906:20: performance:inconclusive: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.h:739:10: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.cpp:2906:20: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/repeat_builder.cpp:3685:27: performance:inconclusive: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.h:922:10: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.cpp:3685:27: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4688:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4688:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4689:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4689:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4690:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4690:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4693:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4693:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4699:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4699:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4705:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4705:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4717:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4717:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4720:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4720:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4723:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4723:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4727:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4727:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4736:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4736:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.cpp:4743:5: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/repeat_builder.cpp:4743:5: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/repeat_builder.h:609:10: performance:inconclusive: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.cpp:1484:17: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.h:609:10: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_builder.h:666:10: performance:inconclusive: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.cpp:1659:20: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.h:666:10: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_builder.h:693:10: performance:inconclusive: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.cpp:2523:20: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.h:693:10: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_builder.h:739:10: performance:inconclusive: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.cpp:2906:20: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.h:739:10: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_builder.h:922:10: performance:inconclusive: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/repeat_builder.cpp:3685:27: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/repeat_builder.h:922:10: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/repeat_kmer.h:207:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/repeat_kmer.h:243:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/repeat_kmer.h:281:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/repeat_kmer.h:512:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sam.h:177:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/sam.h:177:7: performance:inconclusive: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/sam.h:282:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/sam.h:282:7: performance:inconclusive: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/sam.h:417:26: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/sam.h:417:26: performance:inconclusive: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/sam.h:469:26: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
head hisat2-2.2.1/sam.h:469:26: performance:inconclusive: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/splice_site.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/splice_site.cpp:605:20: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
     hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
     hisat2-2.2.1/splice_site.cpp:605:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
2.17.0 hisat2-2.2.1/splice_site.h:583:10: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
     hisat2-2.2.1/splice_site.cpp:605:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
     hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
2.17.0 hisat2-2.2.1/splice_site.h:583:10: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
     hisat2-2.2.1/splice_site_new.cpp:1001:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
     hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
2.17.0 hisat2-2.2.1/splice_site_new.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/splice_site_new.cpp:1001:20: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
     hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
     hisat2-2.2.1/splice_site_new.cpp:1001:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
head hisat2-2.2.1/spliced_aligner.h:1525:52: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/spliced_aligner.h:1525:53: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/spliced_aligner.h:843:52: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/spliced_aligner.h:843:53: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/sse_util.cpp:27:20: performance:inconclusive: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sse_util.h:510:7: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sse_util.cpp:27:20: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/sse_util.h:410:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/sse_util.h:410:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/sse_util.h:410:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/sse_util.h:487:25: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/sse_util.h:487:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/sse_util.h:487:48: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/sse_util.h:510:7: performance:inconclusive: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     hisat2-2.2.1/sse_util.cpp:27:20: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
     hisat2-2.2.1/sse_util.h:510:7: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
2.17.0 hisat2-2.2.1/sstring.h:119:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:119:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:153:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:256:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:256:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:277:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:327:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:327:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:348:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:372:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:372:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:398:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:398:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:419:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:443:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:443:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/sstring.h:469:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:469:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head hisat2-2.2.1/sstring.h:88:17: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/sstring.h:88:18: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/sstring.h:94:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 hisat2-2.2.1/unique.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head hisat2-2.2.1/word_io.h:106:15: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/word_io.h:106:16: style: C-style pointer casting [cstyleCast]
2.17.0 hisat2-2.2.1/word_io.h:115:10: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:115:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:165:10: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:165:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:215:10: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:215:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:265:10: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:265:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/word_io.h:321:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:321:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:331:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head hisat2-2.2.1/word_io.h:37:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:37:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:45:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:45:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:55:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:55:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:63:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:63:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:73:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:73:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:81:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:81:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:91:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:91:13: style: C-style pointer casting [cstyleCast]
head hisat2-2.2.1/word_io.h:99:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 hisat2-2.2.1/word_io.h:99:13: style: C-style pointer casting [cstyleCast]


DONE