2022-06-27 22:54
ftp://ftp.de.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -D__GNUC__ --platform=unix64 -rp=temp -j1
platform: Linux-5.4.0-121-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.24
compiler: g++ (Ubuntu 10.3.0-1ubuntu1~20.04) 10.3.0
cppcheck: head 2.8
head-info: cdeebc1 (2022-06-27 20:55:09 +0200)
count: 144 144
elapsed-time: 144.8 184.8
head-timing-info:
 Tokenizer::simplifyTokens1: 46.3727s (avg. 0.445891s - 104 result(s))
 Tokenizer::simplifyTokens1::ValueFlow: 45.4709s (avg. 0.43722s - 104 result(s))
 Tokenizer::simplifyTokens1::createSymbolDatabase: 0.538347s (avg. 0.00517641s - 104 result(s))
 Check function usage::runChecks: 0.23936s (avg. 0.00230154s - 104 result(s))
 Tokenizer::createTokens: 0.1473s (avg. 0.00141635s - 104 result(s))
 Overall time: 93.3982s

old-timing-info:
 Tokenizer::simplifyTokens1: 59.5869s (avg. 0.572951s - 104 result(s))
 Tokenizer::simplifyTokens1::ValueFlow: 58.6808s (avg. 0.564238s - 104 result(s))
 Tokenizer::simplifyTokens1::createSymbolDatabase: 0.549535s (avg. 0.00528399s - 104 result(s))
 Check function usage::runChecks: 0.245002s (avg. 0.00235579s - 104 result(s))
 Tokenizer::createTokens: 0.150537s (avg. 0.00144747s - 104 result(s))
 Overall time: 119.825s

head results:
genomethreader-1.7.3/src/gth/ags.c:21:17: style: struct member 'GthAGSObject::pgl' is never used. [unusedStructMember]
genomethreader-1.7.3/src/gth/align_dna.c:420:13: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/align_dna.c:418:13: note: First condition
genomethreader-1.7.3/src/gth/align_dna.c:420:13: note: Second condition
genomethreader-1.7.3/src/gth/align_dna.c:194:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:186:11: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:194:9: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:202:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:194:9: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:202:9: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:211:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:205:11: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:211:9: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:217:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:211:9: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:217:9: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:392:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:382:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:392:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:399:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:392:13: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:399:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:413:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:403:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:413:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:422:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_dna.c:413:13: note: value is assigned
genomethreader-1.7.3/src/gth/align_dna.c:422:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_dna.c:55:41: style: Parameter 'jump_table' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/align_dna.c:159:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/align_dna.c:297:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/align_dna.c:723:14: style: Variable 'maxvalue' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/align_dna.c:728:13: style: Variable 'value' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/align_protein.c:372:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:365:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:372:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:381:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:374:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:381:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:398:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:392:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:398:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:407:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:400:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:407:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:416:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:409:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:416:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:425:13: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/gth/align_protein.c:418:15: note: value is assigned
genomethreader-1.7.3/src/gth/align_protein.c:425:13: note: value is overwritten
genomethreader-1.7.3/src/gth/align_protein.c:123:64: style: Parameter 'jump_table' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/align_protein.c:1006:12: style: Variable 'maxvalue' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/align_protein.c:1010:11: style: Variable 'value' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/backtrace_path.c:215:52: style: Parameter 'cutoffs' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/backtrace_path.c:221:72: style: Parameter 'cutoffs' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/bssm_seq_processor.c:347:42: style: Same expression 'seqid' found multiple times in chain of '&&' operators. [duplicateExpression]
genomethreader-1.7.3/src/gth/bssm_train_visitor.c:225:7: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/gth/bssm_train_visitor.c:222:17: note: Assignment 'had_err=0', assigned value is 0
genomethreader-1.7.3/src/gth/bssm_train_visitor.c:225:7: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/gth/chaining.c:424:36: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/chaining.c:418:36: note: First condition
genomethreader-1.7.3/src/gth/chaining.c:424:36: note: Second condition
genomethreader-1.7.3/src/gth/compute_scores.c:232:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/compute_scores.c:354:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/compute_scores.c:406:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/compute_scores.c:407:35: style: Variable 'dp_options_est' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/editoperation.c:71:16: warning: Identical inner 'return' condition is always true. [identicalInnerCondition]
genomethreader-1.7.3/src/gth/editoperation.c:70:11: note: outer condition: eop&maxlen
genomethreader-1.7.3/src/gth/editoperation.c:71:16: note: identical inner condition: eop&maxlen
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:291:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:279:7: note: First condition
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:291:7: note: Second condition
genomethreader-1.7.3/src/gth/gt_gthsplit.c:206:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/gt_gthsplit.c:198:7: note: First condition
genomethreader-1.7.3/src/gth/gt_gthsplit.c:206:7: note: Second condition
genomethreader-1.7.3/src/gth/gthalignment.c:73:52: style: Parameter 'alignmentstart' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthalignment.c:976:44: style: Parameter 'genomicproteinline' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthalignment.c:977:44: style: Parameter 'referenceproteinline' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthorf.c:314:14: style: Expression is always true because 'else if' condition is opposite to previous condition at line 310. [multiCondition]
genomethreader-1.7.3/src/gth/gthorf.c:310:12: note: first condition
genomethreader-1.7.3/src/gth/gthorf.c:314:14: note: else if condition is opposite to first condition
genomethreader-1.7.3/src/gth/gthorf.c:79:7: warning: Either the condition 'orfA' is redundant or there is possible null pointer dereference: orfA. [nullPointerRedundantCheck]
genomethreader-1.7.3/src/gth/gthorf.c:78:13: note: Assuming that condition 'orfA' is not redundant
genomethreader-1.7.3/src/gth/gthorf.c:76:22: note: Assignment to 'orfA=(struct MaximalORF*)dataA'
genomethreader-1.7.3/src/gth/gthorf.c:76:20: note: orfA is assigned '(struct MaximalORF*)dataA' here.
genomethreader-1.7.3/src/gth/gthorf.c:79:7: note: Null pointer dereference
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:122:53: style: Parameter 'oldstate' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:44:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:45:35: style: Variable 'dp_options_est' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:62:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:63:35: style: Variable 'dp_options_est' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:80:37: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:81:35: style: Variable 'dp_options_est' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthtrans.c:96:37: style: Parameter 'template_in' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthtrans.c:97:37: style: Parameter 'frame0_in' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthtrans.c:98:37: style: Parameter 'frame1_in' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/gthtrans.c:99:37: style: Parameter 'frame2_in' can be declared as pointer to const [constParameter]
genomethreader-1.7.3/src/gth/input.c:799:41: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
genomethreader-1.7.3/src/gth/parse_options.c:266:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:257:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:266:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:274:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:266:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:274:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:302:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:294:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:302:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:337:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:330:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:337:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:344:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:337:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:344:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:352:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:344:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:352:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:362:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:352:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:362:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:371:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:362:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:371:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:568:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:557:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:568:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:578:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:568:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:578:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:588:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:578:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:588:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:599:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:588:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:599:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:609:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:599:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:609:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:618:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:609:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:618:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:629:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:618:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:629:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:639:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:629:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:639:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:649:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:639:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:649:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:659:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:649:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:659:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:674:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:659:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:674:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:689:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:674:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:689:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:705:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:689:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:705:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:717:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:705:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:717:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:728:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:717:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:728:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:737:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:728:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:737:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:749:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:737:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:749:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:761:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:749:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:761:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:794:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:780:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:794:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:806:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:794:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:806:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:817:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:806:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:817:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:828:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:817:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:828:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:841:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:828:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:841:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:851:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:841:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:851:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:862:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:851:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:862:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:873:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:862:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:873:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:883:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:873:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:883:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:894:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:883:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:894:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:905:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:894:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:905:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:916:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:905:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:916:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:928:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:916:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:928:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:960:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:948:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:960:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:973:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:960:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:973:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:985:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:973:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:985:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:996:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:985:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:996:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1006:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:996:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1006:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1017:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1006:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1017:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1026:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1017:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1026:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1036:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1026:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1036:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1047:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1036:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1047:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1058:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1047:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1058:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1070:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1058:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1070:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1084:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1070:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1084:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1095:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1084:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1095:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1107:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1095:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1107:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1119:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1107:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1119:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1133:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1119:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1133:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1146:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1133:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1146:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1157:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1146:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1157:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1243:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1233:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1243:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1254:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1243:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1254:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1264:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1254:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1264:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1275:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1264:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1275:7: note: Second condition
genomethreader-1.7.3/src/gth/parse_options.c:1566:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/gth/parse_options.c:1548:7: note: First condition
genomethreader-1.7.3/src/gth/parse_options.c:1566:7: note: Second condition
genomethreader-1.7.3/src/gth/pgl.c:24:8: style: struct member 'GthPGLObject::gen_strand_forward' is never used. [unusedStructMember]
genomethreader-1.7.3/src/gth/pgl.c:176:7: style: Variable 'ags' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/similarity_filter.c:645:32: style: Variable 'gen_offset' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/time.c:42:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:278:14: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:257:14: note: First condition
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:278:14: note: Second condition
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:366:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:330:7: note: First condition
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:366:7: note: Second condition
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:322:7: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:306:17: note: Assignment 'had_err=0', assigned value is 0
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:322:7: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:335:12: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:330:7: note: Assuming that condition '!had_err' is not redundant
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:335:12: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:345:16: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:330:7: note: Assuming that condition '!had_err' is not redundant
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:345:16: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:370:12: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:366:7: note: Assuming that condition '!had_err' is not redundant
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:370:12: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:376:21: style: Condition '!had_err' is always true [knownConditionTrueFalse]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:366:7: note: Assuming that condition '!had_err' is not redundant
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:376:21: note: Condition '!had_err' is always true
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:515:46: warning: Logical disjunction always evaluates to true: isreferencefile && proteinsmap || !(isreferencefile && proteinsmap). [incorrectLogicOperator]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:453:7: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:424:7: note: First condition
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:453:7: note: Second condition
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:164:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:177:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:204:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:209:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:515:46: style: Opposite expression on both sides of '||'. [oppositeExpression]
genomethreader-1.7.3/src/libgenomethreader/jt.c:127:15: style: Local variable 'elem' shadows outer variable [shadowVariable]
genomethreader-1.7.3/src/libgenomethreader/jt.c:68:10: note: Shadowed declaration
genomethreader-1.7.3/src/libgenomethreader/jt.c:127:15: note: Shadow variable
genomethreader-1.7.3/src/libgenomethreader/jt.c:237:15: style: Local variable 'elem' shadows outer variable [shadowVariable]
genomethreader-1.7.3/src/libgenomethreader/jt.c:221:11: note: Shadowed declaration
genomethreader-1.7.3/src/libgenomethreader/jt.c:237:15: note: Shadow variable
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:374:15: style: The if condition is the same as the previous if condition [duplicateCondition]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:372:15: note: First condition
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:374:15: note: Second condition
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:62:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:54:11: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:62:9: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:70:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:62:9: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:70:9: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:79:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:73:11: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:79:9: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:85:9: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:79:9: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:85:9: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:351:15: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:344:15: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:351:15: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:376:15: style: Variable 'value' is reassigned a value before the old one has been used. [redundantAssignment]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:367:15: note: value is assigned
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:376:15: note: value is overwritten
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:27:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:181:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
diff:
head genomethreader-1.7.3/src/gth/align_dna.c:55:41: style: Parameter 'jump_table' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/align_dna.c:55:41: style: Parameter 'jump_table' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/align_protein.c:123:64: style: Parameter 'jump_table' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/align_protein.c:123:64: style: Parameter 'jump_table' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/backtrace_path.c:215:52: style: Parameter 'cutoffs' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/backtrace_path.c:215:52: style: Parameter 'cutoffs' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/backtrace_path.c:221:72: style: Parameter 'cutoffs' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/backtrace_path.c:221:72: style: Parameter 'cutoffs' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthalignment.c:73:52: style: Parameter 'alignmentstart' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthalignment.c:73:52: style: Parameter 'alignmentstart' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthalignment.c:976:44: style: Parameter 'genomicproteinline' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthalignment.c:976:44: style: Parameter 'genomicproteinline' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthalignment.c:977:44: style: Parameter 'referenceproteinline' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthalignment.c:977:44: style: Parameter 'referenceproteinline' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthsplicesitescr.c:122:53: style: Parameter 'oldstate' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthsplicesitescr.c:122:53: style: Parameter 'oldstate' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthtrans.c:96:37: style: Parameter 'template_in' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthtrans.c:96:37: style: Parameter 'template_in' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthtrans.c:97:37: style: Parameter 'frame0_in' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthtrans.c:97:37: style: Parameter 'frame0_in' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthtrans.c:98:37: style: Parameter 'frame1_in' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthtrans.c:98:37: style: Parameter 'frame1_in' can be declared with const [constParameter]
head genomethreader-1.7.3/src/gth/gthtrans.c:99:37: style: Parameter 'frame2_in' can be declared as pointer to const [constParameter]
2.8 genomethreader-1.7.3/src/gth/gthtrans.c:99:37: style: Parameter 'frame2_in' can be declared with const [constParameter]


DONE