2025-06-27 13:26
ftp://ftp.de.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --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: 286 280
elapsed-time: 0.8 0.8
head-timing-info:

old-timing-info:

head results:
genomethreader-1.7.3/src/gth/ags.c:35:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GthExonAGS [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags.c:102:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_STRAND_REVERSE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags.c:145:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable donorsiteprob [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags.c:152:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable acceptorsiteprob [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/bssm_helper.c:27:25: error: There is an unknown macro here somewhere. Configuration is required. If GT_DNABASES is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/ags_build.c:290:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags_build.c:349:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable range [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags_build.c:409:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable successorintron [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/align_protein.c:767:44: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/align_dna.c:606:44: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/bssm_param_rmsd.c:30:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HYPOTHESIS7 [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/bssm_param.c:562:59: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/call_info.c:34:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_TRANSLATIONTABLE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/bssm_seq_processor.c:1291:21: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/bssm_train_visitor.c:104:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/bssm_train_visitor.c:151:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_NUM_OF_STRAND_TYPES [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/ags_build.c:119:51: style: Parameter 'nodeA' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/ags_build.c:119:68: style: Parameter 'nodeB' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/ags_build.c:157:53: style: Parameter 'nodeA' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/ags_build.c:157:70: style: Parameter 'nodeB' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/ags_build.c:291:18: style: Variable 'exonscoreinfo' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/chaining.c:154:40: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/dp_options_core.c:26:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_NOICININTRONCHECK [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:68:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Editoperation [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:80:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:87:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:93:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:100:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:106:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_WORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:113:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:171:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:230:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:237:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:256:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROTEIN_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:338:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:345:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTIONEOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:352:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXIDENTICALLENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:448:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXIDENTICALLENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:555:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:566:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:582:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISMATCHEOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:590:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETIONEOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:598:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTIONEOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:606:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETIONEOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:625:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISMATCH_WITH_1_GAP_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:634:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISMATCH_WITH_2_GAPS_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:643:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETION_WITH_1_GAP_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:652:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETION_WITH_2_GAPS_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:662:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETION_WITH_1_GAP_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:685:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELETION_WITH_2_GAPS_EOP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:709:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROTEIN_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:720:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROTEIN_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:734:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:746:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:796:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOP_TYPE_INTRON_WITH_1_BASE_LEFT [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:850:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROTEIN_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:858:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Editoperation [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:866:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:878:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:888:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:915:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:976:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:1099:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/backtrace_path.c:1120:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_options_postpro.c:26:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_RELAXED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_options_est.c:25:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_PROBIES [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/chain_collection.c:51:13: style: Variable 'chainA' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/chain_collection.c:52:13: style: Variable 'chainB' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/dp_scores_protein.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DASH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_scores_protein.c:82:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/editoperation.c:25:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXIDENTICALLENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/editoperation.c:69:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXIDENTICALLENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/editoperation.c:79:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXIDENTICALLENGTH [valueFlowBailoutIncompleteVar]
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/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/gff3_pgl_visitor.c:103:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gff3_pgl_visitor.c:235:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTHSOURCETAG [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gff3_sa_visitor.c:78:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_ft_gene [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gff3_sa_visitor.c:164:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTHSOURCETAG [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/compute_scores.c:57:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/compute_scores.c:159:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/compute_scores.c:387:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DASH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/compute_scores.c:654:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gth.c:69:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INITIAL_XML_INDENTLEVEL [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmprint.c:54:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_versionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmprint.c:78:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmbuild.c:122:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_OPTION_PARSER_OK [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmbuild.c:168:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_DONOR_TYPE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmbuild.c:199:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_versionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmfileinfo.c:43:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_versionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmfileinfo.c:67:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BSSMFILEENDING [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthconsensus.c:126:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INITIAL_XML_INDENTLEVEL [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_param.c:70:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_WILDCARD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_param.c:303:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_param.c:486:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_param.c:534:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GthFlt [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/dp_param.c:581:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtRange [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthfilestat.c:32:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FILE_MODE_UNCOMPRESSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthfilestat.c:73:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gth_show_on_stdout [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthfilestat.c:101:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DC_NONE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:57:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FILE_MODE_UNCOMPRESSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:96:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_ft_exon [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:169:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FILE_MODE_GZIP [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthbssmtrain.c:269:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_PATH_SEPARATOR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthmkbssmfiles.c:39:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gt_versionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthmkbssmfiles.c:64:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_PATH_SEPARATOR [valueFlowBailoutIncompleteVar]
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/gthalignment.c:1138:42: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/gt_gthsplit.c:180:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FORCE_OPT_CSTR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthsplit.c:219:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FILE_MODE_UNCOMPRESSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthsplit.c:280:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FORCE_OPT_CSTR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gt_gthsplit.c:352:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtUword [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthchain.c:412:31: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/gthcluster.c:27:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable leftgenomicexonborder [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthcluster.c:45:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthcluster.c:73:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthcluster.c:96:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthcluster.c:158:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthcutoffsminimal.c:59:23: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthcutoffsrelaxed.c:58:23: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthmatch.c:20:38: style: Parameter 'match1' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/gthmatch.c:20:56: style: Parameter 'match2' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/gthcutoffsstrict.c:72:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_CODON_LENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthorf.c:143:52: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/gthcutoffsstrict.c:91:22: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthoutput.c:24:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GthOutput [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsadistri.c:43:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable leftgenomicexonborder [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsortags.c:25:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_UNDEF_GTHDBL [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsortags.c:45:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:66:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DASH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsadistri.c:23:13: style: Variable 'exoninfo' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsortags.c:23:11: style: Variable 'agsA' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsortags.c:24:11: style: Variable 'agsB' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsortags.c:39:22: style: Variable 'splicesiteprob' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthtrans.c:187:37: error: There is an unknown macro here somewhere. Configuration is required. If GT_WUS is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/gthverbosefunc.c:23:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMENTCHAR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:38:56: style: Parameter 'state' can be declared as pointer to const. However it seems that 'calcsplicesitescoreprocmismatchordeletion' is a callback function, if 'state' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:136:36: note: You might need to cast the function pointer here
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:38:56: note: Parameter 'state' can be declared as pointer to const
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:45:20: style: Variable 'dp_options_est' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:56:70: style: Parameter 'state' can be declared as pointer to const. However it seems that 'calcsplicesitescoreprocinsertion' is a callback function, if 'state' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:137:36: note: You might need to cast the function pointer here
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:56:70: note: Parameter 'state' can be declared as pointer to const
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:63:20: style: Variable 'dp_options_est' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:76:66: style: Parameter 'state' can be declared as pointer to const. However it seems that 'calcsplicesitescoreprocmatch' is a callback function, if 'state' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:138:36: note: You might need to cast the function pointer here
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:76:66: note: Parameter 'state' can be declared as pointer to const
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:81:20: style: Variable 'dp_options_est' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:117:28: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/gthsplicesitescr.c:122:53: style: Parameter 'oldstate' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/gthtravalign.c:70:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_CODON_LENGTH [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthtravalign.c:144:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_CODON_LENGTH [valueFlowBailoutIncompleteVar]
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:44:16: style: Variable 'gen_alphabet_mapsize' 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:62:16: style: Variable 'gen_alphabet_mapsize' 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/gthsplicesitescr.c:80:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/gthverbosefuncvm.c:23:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMENTCHAR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/gthverbosefuncvm.c:21:38: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/gthxml.c:28:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_SPLICED_ALIGNMENT_XML_VERSION [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/input.c:290:36: error: There is an unknown macro here somewhere. Configuration is required. If GT_WUS is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/intermediate.c:134:3: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
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/md5_cache.c:64:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTHNOFLOCKENVNAME [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/path_walker.c:236:68: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/compute_scores.c:35:47: style: Parameter 'dp_param' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/compute_scores.c:102:49: style: Parameter 'dp_param' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/compute_scores.c:407:20: style: Variable 'dp_options_est' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/parse_options.c:1484:29: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
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:232:16: 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:354:16: 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/compute_scores.c:406:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
genomethreader-1.7.3/src/gth/pgl.c:43:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl.c:92:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl.c:127:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UINT [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl.c:167:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtUword [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/path_matrix.c:47:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl.c:191:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_STRAND_REVERSE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/path_matrix.c:139:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_WUS [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/path_matrix.c:180:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable on_max_path_e [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl.c:169:11: style: Variable 'ags' can be declared as pointer to const [constVariablePointer]
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/pgl_collection.c:57:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtRange [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl_collection.c:101:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GthSACluster [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl_collection.c:145:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gth_sa_cmp_genomic_actual [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/pgl_collection.c:186:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UINT [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/proc_sa_collection.c:102:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UINT [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/region_factory.c:41:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtUword [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/region_factory.c:88:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/region_factory.c:112:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/region_factory.c:180:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_UWORD [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/region_factory.c:238:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/run_header.c:110:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/run_header.c:179:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMENTCHAR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/path_matrix.c:37:76: style: Parameter 'ri' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/sa.c:205:31: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/sa_cmp.c:22:36: style: Parameter 'rangeA' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/sa_cmp.c:22:53: style: Parameter 'rangeB' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/gth/sa_filter.c:37:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_MIN_ALIGNMENTSCORE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_filter.c:137:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_MIN_ALIGNMENTSCORE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/similarity_filter.c:73:30: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/sa_collection.c:99:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DC_NONE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_collection.c:177:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DC_NONE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_collection.c:249:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_collection.c:277:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gth_sa_delete [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_collection.c:304:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DC_NONE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/sa_collection.c:458:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/splice_site_model.c:33:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_DEFAULT_DISABLEU12INTRONMODEL [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/splice_site_model.c:82:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BSSMFILEENDING [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/spliced_seq.c:32:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/spliced_seq.c:45:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/spliced_seq.c:72:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtUword [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/spliced_seq.c:101:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMENTCHAR [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/spliced_seq.c:160:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GtUword [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/gth/stat.c:304:37: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/time.c:29:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNUSED [valueFlowBailoutIncompleteVar]
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/gth/spliced_seq.c:156:12: style: Variable 'splicedposptr' can be declared as pointer to const [constVariablePointer]
genomethreader-1.7.3/src/gth/txt_pgl_visitor.c:44:33: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/txt_sa_visitor.c:64:39: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/xml_final_sa_visitor.c:95:46: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/xml_inter_sa_visitor.c:87:43: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gth/xml_pgl_visitor.c:43:51: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/gthunit.c:27:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lm_license [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gt_align_dna.c:45:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gthversionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gt_align_dna.c:71:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNDEF_ULONG [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpolyafunc.c:30:42: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/libgenomethreader/gthversionfunc.c:12:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTH_VERSION [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthmkvtree.c:55:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTHDATAENVNAME [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthmkvtree.c:97:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_MAX [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthmkvtree.c:260:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TISTAB [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthvmatch.c:94:67: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:126:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:148:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_FILE_MODE_UNCOMPRESSED [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:235:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gthversionfunc [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gt_gthgetseq.c:338:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:74:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_MAX [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:149:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:228:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_MAX [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:491:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:508:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TISTAB [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:651:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROTEIN_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:682:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_ALPHA [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/jt.c:46:26: error: There is an unknown macro here somewhere. Configuration is required. If GT_WU is a macro then please configure it. [unknownMacro]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:38:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_E_STATE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:127:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_E_STATE [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:208:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DNA_E_NM [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:22:65: style: Parameter 'dpm' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:23:74: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:29:64: style: Parameter 'dp_param' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:31:53: style: Parameter 'dp_options_core' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:33:53: style: Parameter 'dp_scores_protein' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:34:66: style: Parameter 'jump_table' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_protein.c:35:61: style: Parameter 'gen_ranges' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/seq_con_multiseq.c:42:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/seq_con_multiseq.c:58:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable False [valueFlowBailoutIncompleteVar]
genomethreader-1.7.3/src/libgenomethreader/seq_con_multiseq.c:244:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
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/gthpre.c:52:43: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/gthpre.c:70:57: style: Parameter 'indexname' can be declared as pointer to const [constParameterPointer]
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:20:35: style: Parameter 'dp_options_est' can be declared as pointer to const [constParameterPointer]
genomethreader-1.7.3/src/libgenomethreader/jt_align_dna.c:21:36: style: Parameter 'dp_options_core' can be declared as pointer to const [constParameterPointer]
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/compute_scores.c:232:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
head genomethreader-1.7.3/src/gth/compute_scores.c:354:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
head genomethreader-1.7.3/src/gth/compute_scores.c:406:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
head genomethreader-1.7.3/src/gth/gthsplicesitescr.c:44:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
head genomethreader-1.7.3/src/gth/gthsplicesitescr.c:62:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]
head genomethreader-1.7.3/src/gth/gthsplicesitescr.c:80:16: style: Variable 'gen_alphabet_mapsize' is assigned a value that is never used. [unreadVariable]


DONE