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To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/AssessPhasing.scala"},"region":{"startLine":627}}}],"partialFingerprints":{"codehealthFindingId/v1":"d064cbf62d36cbbac3c796be2d7fe1e357ba87c68c34c7b01e7172542ba2d233"}},{"ruleId":"D2","level":"warning","message":{"text":"VanillaUmiConsensusCaller.consensusCall (cognitive 46): VanillaUmiConsensusCaller.consensusCall has cognitive complexity 46 (threshold 15). Drivers by points: if/else 19 (43 pts), loops 1 (3 pts) (nesting depth added 26). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. 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To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/MakeTwoSampleMixtureVcf.scala"},"region":{"startLine":103}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac47421ab0c573532ef44f68aacb150183ba5a93a0ec7a8146aa690f9348e323"}},{"ruleId":"D2","level":"warning","message":{"text":"PickIlluminaIndicesCommand.execute (cognitive 40): PickIlluminaIndicesCommand.execute has cognitive complexity 40 (threshold 15). Drivers by points: if/else 14 (24 pts), loops 8 (13 pts), boolean chains 1, error handling 1, ternaries 1 (nesting depth added 15). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/java/com/fulcrumgenomics/util/PickIlluminaIndicesCommand.java"},"region":{"startLine":234}}}],"partialFingerprints":{"codehealthFindingId/v1":"ea3fa8a048f242acefbc4625a92e633e72067cf1e9ff009d9c5b81de0dfb7f01"}},{"ruleId":"D2","level":"warning","message":{"text":"CorrectUmis.execute (cognitive 36): CorrectUmis.execute has cognitive complexity 36 (threshold 15). Drivers by points: if/else 15 (29 pts), match/switch 2 (5 pts), boolean chains 2 (nesting depth added 17). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/CorrectUmis.scala"},"region":{"startLine":166}}}],"partialFingerprints":{"codehealthFindingId/v1":"bd81159ef1449eda8ce81fe9a872d7381a3bf11a67b6b42da78f2b4e203138e9"}},{"ruleId":"D2","level":"warning","message":{"text":"PhaseCigar.toIlluminaSwitchErrorsHmm (cognitive 36): PhaseCigar.toIlluminaSwitchErrorsHmm has cognitive complexity 36 (threshold 15). Drivers by points: if/else 25 (33 pts), loops 2, boolean chains 1 (nesting depth added 8). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/AssessPhasing.scala"},"region":{"startLine":897}}}],"partialFingerprints":{"codehealthFindingId/v1":"7a9a9ad9b3e0f613b1892dd97d3565a0430abf22930886621c3af71ca58b6df5"}},{"ruleId":"D2","level":"warning","message":{"text":"SamRecordClipper.upgradeClipping (cognitive 34): SamRecordClipper.upgradeClipping has cognitive complexity 34 (threshold 15). Drivers by points: if/else 11 (25 pts), match/switch 2 (7 pts), boolean chains 2 (nesting depth added 19). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/SamRecordClipper.scala"},"region":{"startLine":512}}}],"partialFingerprints":{"codehealthFindingId/v1":"abd7d24838811db93d63160e770c37901d5237dc22ccf2ff6d64dbabe0193ea0"}},{"ruleId":"D2","level":"warning","message":{"text":"ExtractUmisFromBam.execute (cognitive 34): ExtractUmisFromBam.execute has cognitive complexity 34 (threshold 15). Drivers by points: if/else 12 (33 pts), loops 1 (nesting depth added 21). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/ExtractUmisFromBam.scala"},"region":{"startLine":135}}}],"partialFingerprints":{"codehealthFindingId/v1":"696ff3b399a6d8c7e068d86facdc242bf101d78ccaa0c91145c811ed0f935819"}},{"ruleId":"D2","level":"warning","message":{"text":"TrimPrimers.trimReadsForTemplate (cognitive 32): TrimPrimers.trimReadsForTemplate has cognitive complexity 32 (threshold 15). Drivers by points: if/else 13 (22 pts), match/switch 3 (6 pts), boolean chains 4 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/TrimPrimers.scala"},"region":{"startLine":182}}}],"partialFingerprints":{"codehealthFindingId/v1":"f208b2678ee211ef6b0eef9feae8d97c3a9769d5a1cb960baef6337b8e2e4600"}},{"ruleId":"D2","level":"warning","message":{"text":"VcfConversions.toScalaVariant (cognitive 28): VcfConversions.toScalaVariant has cognitive complexity 28 (threshold 15). Drivers by points: if/else 17 (21 pts), match/switch 2 (4 pts), boolean chains 2, error handling 1 (nesting depth added 6). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala"},"region":{"startLine":205}}}],"partialFingerprints":{"codehealthFindingId/v1":"abcd0c1f1bedd871a0e7b1258e29c9566a68e80b9537ffb6f9eb6ef0adab2667"}},{"ruleId":"D2","level":"warning","message":{"text":"Alignment.sub (cognitive 25): Alignment.sub has cognitive complexity 25 (threshold 15). Drivers by points: if/else 13 (23 pts), boolean chains 2 (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala"},"region":{"startLine":457}}}],"partialFingerprints":{"codehealthFindingId/v1":"689f4e2500253124eeb6db5aeca767f4747bff74ae2d023b56130d798ef0f9a8"}},{"ruleId":"D2","level":"warning","message":{"text":"SamRecordClipper.clip (cognitive 25): SamRecordClipper.clip has cognitive complexity 25 (threshold 15). Drivers by points: if/else 10 (17 pts), boolean chains 4, match/switch 1 (3 pts), loops 1 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/SamRecordClipper.scala"},"region":{"startLine":412}}}],"partialFingerprints":{"codehealthFindingId/v1":"d20a347204be1cb1aab8b4b9e2c95bfdac6c6518773574dacb85f3a615d2db55"}},{"ruleId":"D2","level":"warning","message":{"text":"FindTechnicalReads.execute (cognitive 24): FindTechnicalReads.execute has cognitive complexity 24 (threshold 15). Drivers by points: loops 3 (10 pts), if/else 5 (8 pts), match/switch 2 (4 pts), boolean chains 2 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/FindTechnicalReads.scala"},"region":{"startLine":77}}}],"partialFingerprints":{"codehealthFindingId/v1":"334b4a83aa9d73e3aa83f888e5a41c0fc13cbd37a4736b5c67c0e573fadb130e"}},{"ruleId":"D2","level":"warning","message":{"text":"DuplexConsensusCaller.duplexConsensus (cognitive 23): DuplexConsensusCaller.duplexConsensus has cognitive complexity 23 (threshold 15). Drivers by points: if/else 13 (20 pts), boolean chains 2, match/switch 1 (nesting depth added 7). The drivers above price the dispatch low by construction \u2014 a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full \u2014 so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/DuplexConsensusCaller.scala"},"region":{"startLine":396}}}],"partialFingerprints":{"codehealthFindingId/v1":"447281f13b38bb2c0394a61c4d0f3405b5f50aaf625fc19ba76cfd7371692d19"}},{"ruleId":"D2","level":"warning","message":{"text":"PileupBuilder.build (cognitive 21): PileupBuilder.build has cognitive complexity 21 (threshold 15). Drivers by points: if/else 13 (17 pts), boolean chains 4 (nesting depth added 4). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala"},"region":{"startLine":193}}}],"partialFingerprints":{"codehealthFindingId/v1":"5d325431f0dec1f41edc89451889ae97cee54ed293c8b3199eba85d1692cf3b3"}},{"ruleId":"D2","level":"warning","message":{"text":"AssignPrimers.execute (cognitive 21): AssignPrimers.execute has cognitive complexity 21 (threshold 15). Drivers by points: if/else 12 (14 pts), match/switch 3 (6 pts), boolean chains 1 (nesting depth added 5). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/util/AssignPrimers.scala"},"region":{"startLine":78}}}],"partialFingerprints":{"codehealthFindingId/v1":"6c81be77b1d962ae1ebfe6df62505f6b9403c0e6db449e60c0c205b9872bb7b9"}},{"ruleId":"D2","level":"warning","message":{"text":"CollectAlternateContigNames.execute (cognitive 20): CollectAlternateContigNames.execute has cognitive complexity 20 (threshold 15). Drivers by points: if/else 8 (9 pts), match/switch 5 (8 pts), boolean chains 3 (nesting depth added 4). To reduce it, split the body: this score is breadth rather than depth \u2014 many checks laid out side by side rather than nested inside one another, so inverting conditions into early returns has nothing left to flatten. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/fasta/CollectAlternateContigNames.scala"},"region":{"startLine":155}}}],"partialFingerprints":{"codehealthFindingId/v1":"cc1a8d11a53fa8aab523ccb15ec1e4512c6d303077ddd5e0521de62802b3e79a"}},{"ruleId":"D2","level":"warning","message":{"text":"GroupReadsByUmi.execute (cognitive 20): GroupReadsByUmi.execute has cognitive complexity 20 (threshold 15). Drivers by points: boolean chains 9, if/else 6 (7 pts), match/switch 2 (3 pts), loops 1 (nesting depth added 2). To reduce it, name the conditions: bind each compound test to a well-named local or a small predicate function, so the body reads as a sequence of named decisions rather than a chain of operators."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala"},"region":{"startLine":642}}}],"partialFingerprints":{"codehealthFindingId/v1":"b62a19a7c1d1258792331e7b41199d74f49dc9ebdfa098c8180cc8f2c727ad02"}},{"ruleId":"D2","level":"warning","message":{"text":"UpdateDelimitedFileContigNames.execute (cognitive 20): UpdateDelimitedFileContigNames.execute has cognitive complexity 20 (threshold 15). Drivers by points: if/else 7 (13 pts), match/switch 3 (7 pts) (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/util/UpdateDelimitedFileContigNames.scala"},"region":{"startLine":72}}}],"partialFingerprints":{"codehealthFindingId/v1":"d6970f1ced030b1dc99439e638e950f8caa5c0405fbbf1a60dcff64c707b5c40"}},{"ruleId":"D2","level":"warning","message":{"text":"PhaseBlock.buildOverlapDetector (cognitive 20): PhaseBlock.buildOverlapDetector has cognitive complexity 20 (threshold 15). Drivers by points: if/else 11 (15 pts), match/switch 1 (3 pts), loops 2 (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/AssessPhasing.scala"},"region":{"startLine":395}}}],"partialFingerprints":{"codehealthFindingId/v1":"a5be2744f95d3f3533a876086d6a3098cc87f84d3e7ee828d63b76a0b2a1e79d"}},{"ruleId":"D2","level":"warning","message":{"text":"MakeMixtureVcf.updateAlleleFractionsForSample (cognitive 20): MakeMixtureVcf.updateAlleleFractionsForSample has cognitive complexity 20 (threshold 15). Drivers by points: if/else 10 (17 pts), match/switch 2 (3 pts) (nesting depth added 8). The drivers above price the dispatch low by construction \u2014 a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full \u2014 so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/MakeMixtureVcf.scala"},"region":{"startLine":228}}}],"partialFingerprints":{"codehealthFindingId/v1":"1a8969a3c20b71469ecd825eb9335a609e715335a9a5c548df4ef89127b876f2"}},{"ruleId":"D2","level":"warning","message":{"text":"CollectErccMetrics.execute (cognitive 19): CollectErccMetrics.execute has cognitive complexity 19 (threshold 15). Drivers by points: if/else 10 (11 pts), boolean chains 5, match/switch 2 (3 pts) (nesting depth added 2). To reduce it, split the body: this score is breadth rather than depth \u2014 many checks laid out side by side rather than nested inside one another, so inverting conditions into early returns has nothing left to flatten. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/rnaseq/CollectErccMetrics.scala"},"region":{"startLine":108}}}],"partialFingerprints":{"codehealthFindingId/v1":"ca09e6af99254e2dd67ddaef1ef3acd3941300ea08e2f97e1c32f9d13a7e4c5a"}},{"ruleId":"D2","level":"warning","message":{"text":"Aligner.fillInterior (cognitive 18): Aligner.fillInterior has cognitive complexity 18 (threshold 15). Drivers by points: if/else 8 (14 pts), loops 2 (3 pts), boolean chains 1 (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/alignment/Aligner.scala"},"region":{"startLine":471}}}],"partialFingerprints":{"codehealthFindingId/v1":"fdb6b835f5d3f32b97c2383ea46452d1ffaf0f795226dca0c7ef7828e5661065"}},{"ruleId":"D2","level":"warning","message":{"text":"FindSwitchbackReads.findTandemSwitchback (cognitive 18): FindSwitchbackReads.findTandemSwitchback has cognitive complexity 18 (threshold 15). Drivers by points: if/else 7 (13 pts), match/switch 2 (5 pts) (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/FindSwitchbackReads.scala"},"region":{"startLine":182}}}],"partialFingerprints":{"codehealthFindingId/v1":"7d7973f3376aeaf3cfa78fc2710471dcb9560d854f5e771a27e67f209189877b"}},{"ruleId":"D2","level":"warning","message":{"text":"AdjacencyUmiAssigner.assign (cognitive 18): AdjacencyUmiAssigner.assign has cognitive complexity 18 (threshold 15). Drivers by points: if/else 4 (8 pts), match/switch 1 (5 pts), loops 1 (3 pts), boolean chains 2 (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala"},"region":{"startLine":273}}}],"partialFingerprints":{"codehealthFindingId/v1":"e5d103b3c299152718610cf847dbba2f60a2dd7076a73a450d14701b9d49c0ab"}},{"ruleId":"D2","level":"warning","message":{"text":"AmpliconLabeller.label (cognitive 18): AmpliconLabeller.label has cognitive complexity 18 (threshold 15). Drivers by points: if/else 12 (14 pts), boolean chains 4 (nesting depth added 2). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/util/AssignPrimers.scala"},"region":{"startLine":227}}}],"partialFingerprints":{"codehealthFindingId/v1":"b604730ebe5329d7546fe401d55f955e47a65864eb8fee6e5875ae88f53f1611"}},{"ruleId":"D2","level":"warning","message":{"text":"ErrorRateByReadPosition.computeMetrics (cognitive 17): ErrorRateByReadPosition.computeMetrics has cognitive complexity 17 (threshold 15). Drivers by points: if/else 9 (13 pts), loops 2 (3 pts), boolean chains 1 (nesting depth added 5). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/ErrorRateByReadPosition.scala"},"region":{"startLine":130}}}],"partialFingerprints":{"codehealthFindingId/v1":"b34d91a6472ee204f8ceabcf6b51cc498e38f927954595c124686b6a1e605ae6"}},{"ruleId":"D2","level":"warning","message":{"text":"FastqToBam.makeSamRecords (cognitive 17): FastqToBam.makeSamRecords has cognitive complexity 17 (threshold 15). Drivers by points: if/else 13 (14 pts), boolean chains 1, error handling 1, match/switch 1 (nesting depth added 1). To reduce it, split the body: this score is breadth rather than depth \u2014 many checks laid out side by side rather than nested inside one another, so inverting conditions into early returns has nothing left to flatten. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/fastq/FastqToBam.scala"},"region":{"startLine":171}}}],"partialFingerprints":{"codehealthFindingId/v1":"f4d49507b4b08d4c1837b68c5b1e7937b7ade9974e3b229e632776537d4e7a1b"}},{"ruleId":"D2","level":"warning","message":{"text":"FindSwitchbackReads.execute (cognitive 16): FindSwitchbackReads.execute has cognitive complexity 16 (threshold 15). Drivers by points: if/else 7 (11 pts), match/switch 2 (3 pts), boolean chains 2 (nesting depth added 5). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/FindSwitchbackReads.scala"},"region":{"startLine":325}}}],"partialFingerprints":{"codehealthFindingId/v1":"c81495cddb66c43df85c7fc788fd85982685557bd8e15d273f3effba30ff439a"}},{"ruleId":"D2","level":"warning","message":{"text":"GroupReadsByUmi.umiForRead (cognitive 16): GroupReadsByUmi.umiForRead has cognitive complexity 16 (threshold 15). Drivers by points: if/else 8 (11 pts), boolean chains 4, match/switch 1 (nesting depth added 3). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala"},"region":{"startLine":862}}}],"partialFingerprints":{"codehealthFindingId/v1":"32596e0d9692e0c95ed7f8a8928feb761463f279918289796ed1b6ef084352c7"}},{"ruleId":"D2","level":"warning","message":{"text":"UmiConsensusCaller.filterToMostCommonAlignment (cognitive 16): UmiConsensusCaller.filterToMostCommonAlignment has cognitive complexity 16 (threshold 15). Drivers by points: if/else 9 (16 pts) (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/UmiConsensusCaller.scala"},"region":{"startLine":406}}}],"partialFingerprints":{"codehealthFindingId/v1":"efa5ad17f8b37723643a63b668b47d11ea97e55e6281f0802f617610fd9e2f83"}},{"ruleId":"D2","level":"warning","message":{"text":"MetricBuilder.fromArgMap (cognitive 16): MetricBuilder.fromArgMap has cognitive complexity 16 (threshold 15). Drivers by points: if/else 6 (10 pts), match/switch 2 (3 pts), boolean chains 2, error handling 1 (nesting depth added 5). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/util/MetricBuilder.scala"},"region":{"startLine":138}}}],"partialFingerprints":{"codehealthFindingId/v1":"081f0aafc79bd5c96c297e2bd6fb6e32429591892aeb13914f1c99f9826918e5"}},{"ruleId":"D3","level":"warning","message":{"text":"TooManyMethods: SamRecord: TooManyMethods \u2014 95 methods. The bar is 30 methods; this is 65 over it, 3.17\u00D7 the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala"},"region":{"startLine":82}}}],"partialFingerprints":{"codehealthFindingId/v1":"a08fdacabc95f2b4161dfc18bc5cd44c22fc242810c1144dc567fc27bb7d3964"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: fastq/DemuxFastqs.scala: FileTooLong \u2014 630 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 130 over it, 1.26\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"9352f00ec608dbd1680113fa18c1d077f71d95b1580719aceeb382a8c5c1f7d1"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: vcf/AssessPhasing.scala: FileTooLong \u2014 572 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 72 over it, 1.14\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/AssessPhasing.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"185b935cb837f23b212fea7e77cb5175cdcfd42c24be0f34dc64ba20cddb07bc"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: umi/GroupReadsByUmi.scala: FileTooLong \u2014 513 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 13 over it, 1.03\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"30065540ae328b99306d43829b4cc3b5aacaa643d8fd366a9ab70fc31f1f5cc0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala:137-151 | src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala:153-167 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala"},"region":{"startLine":137}}}],"partialFingerprints":{"codehealthFindingId/v1":"8a71523782bda0289b2afd2499146810f32b684f53d41a5407a57eaa3568d3aa"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): src/main/scala/com/fulcrumgenomics/umi/CallCodecConsensusReads.scala:153-162 | src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala:167-175 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at \u0060src/main/scala/com/fulcrumgenomics/umi/CallCodecConsensusReads.scala:153\u0060 it runs out through the closing brace of the declaration holding it \u2014 the window is that declaration\u0027s tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/CallCodecConsensusReads.scala"},"region":{"startLine":153}}}],"partialFingerprints":{"codehealthFindingId/v1":"d6288727d0ee9df3637ac8beffc1e2e5fa4d10f181a6504648c6522c7dd62d9a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala:238-244 | src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala:257-263 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala:238\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala"},"region":{"startLine":238}}}],"partialFingerprints":{"codehealthFindingId/v1":"6bcdac46b4a420b471ae053ffd6801e1f4c4bd7782206b541790954b96c0dacc"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): src/main/scala/com/fulcrumgenomics/bam/Bams.scala:481-486 | src/main/scala/com/fulcrumgenomics/bam/TrimPrimers.scala:174-179 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at \u0060src/main/scala/com/fulcrumgenomics/bam/Bams.scala:481\u0060 it runs out through the closing brace of the declaration holding it \u2014 the window is that declaration\u0027s tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/Bams.scala"},"region":{"startLine":481}}}],"partialFingerprints":{"codehealthFindingId/v1":"d15b907418343e9369cf7a84e4742397de21072346fa162c7820d3af81f8e89f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala:137-141 | src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala:156-160 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala:137\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala"},"region":{"startLine":137}}}],"partialFingerprints":{"codehealthFindingId/v1":"9d5612259d06fadf6a57cf903f3036389b4cf701be4103c521dca886c8576495"}},{"ruleId":"D16","level":"note","message":{"text":"Off-boarding risk: anonymized user #1: If anonymized user #1 becomes unavailable, 2 significant file(s) lose their only recent owner: src/main/scala/com/fulcrumgenomics/bam/Bams.scala, src/main/scala/com/fulcrumgenomics/umi/ConsensusCaller.scala. Pair on, review, or document these before any departure."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"5b9bfd5450e2021829e8168008f52c1d05e18163e7ca19b9310e354a5fb7abd5"}},{"ruleId":"D16","level":"note","message":{"text":"Further sole-owners (lower concentration): 1 other contributor(s) are each the sole owner of a small amount of code below the off-boarding threshold \u2014 folded into the bus-factor score and metrics (4 single-owned of 129 analysed files in total, counted over production source files of roughly 2,400 bytes or more, excluding vendored, generated and example/demo trees and test files identified by path convention, largest first; 129 of the 150 production source files in this repository met that bar). They are anonymized user #2 (2 file(s)) \u2014 spread or document their files in the same way, at lower priority than the named off-boarding risks above. The files folded here: src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala, src/main/scala/com/fulcrumgenomics/bam/api/SamOrder.scala."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"6eac528f2429e724e1a97ed868f79eefbcf1888dab4af9a9e673429369bb5b2f"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO long-term: methods for 5\u0027end, 3\u0027 end, unclipped 5\u0027 end and unclipped 3\u0027 end \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala"},"region":{"startLine":35}}}],"partialFingerprints":{"codehealthFindingId/v1":"ad07e787ac97e8f82f77f33cceeb6b692cd64653ef90d1fbcfedb23cc6927f51"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO long-term: replacement for alignment blocks? \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala"},"region":{"startLine":36}}}],"partialFingerprints":{"codehealthFindingId/v1":"7032f12cc0669d5f5c6f8bcd78bcd0c306619d02c6eacce3ccad69e62b82d7e9"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO long-term: replace these two methods with methods on [[Cigar]] to save creating alignment blocks in memory \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala"},"region":{"startLine":257}}}],"partialFingerprints":{"codehealthFindingId/v1":"2ec05ee8663646625ade308f0485e5f79a6630ff1e74767de32754c68c3204a0"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Update this to allow partial matches? \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamOrder.scala"},"region":{"startLine":75}}}],"partialFingerprints":{"codehealthFindingId/v1":"d181b337eba0196091e7e3e18ca085e93df6b2a528c029277f149e5bd972e330"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Update this so that if the SS prefix is not SO, discard SS? \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamOrder.scala"},"region":{"startLine":79}}}],"partialFingerprints":{"codehealthFindingId/v1":"b35950f6c3d693ec7a91c7256f24be07b15f013f19ccd34690f7e95c1c6a1440"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/internal/FgMetricsDoclet.scala"},"region":{"startLine":145}}}],"partialFingerprints":{"codehealthFindingId/v1":"bcb42febc5d73a36184b93faf1154d59fa40d0a4946795a155897534daf00106"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/internal/FgMetricsDoclet.scala"},"region":{"startLine":146}}}],"partialFingerprints":{"codehealthFindingId/v1":"5a3849c137b80c0a6262d0813d58784739e7d7d4522f24b60a626154336869c5"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/internal/FgMetricsDoclet.scala"},"region":{"startLine":147}}}],"partialFingerprints":{"codehealthFindingId/v1":"3f0c4b7f2bd9fd9b2ead94af29dfd4160ddb3ef41725fc5f2de6012c09e5b956"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/internal/FgMetricsDoclet.scala"},"region":{"startLine":149}}}],"partialFingerprints":{"codehealthFindingId/v1":"d6a9d64fe2289f2d1dd190649142011f4fc077f51496ad6bb969c333e547944d"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: better handling of entity links? \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/internal/FgMetricsDoclet.scala"},"region":{"startLine":157}}}],"partialFingerprints":{"codehealthFindingId/v1":"2964a7014de6f86ad4ede21915197acb1a12e7f7b03a7953335810d68e398b87"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: handle chimeric reads or reads with one unmapped etc. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/CodecConsensusCaller.scala"},"region":{"startLine":184}}}],"partialFingerprints":{"codehealthFindingId/v1":"5ae72c6ee57bccc421b60c48a5e84595bc3523d07b65e94cc9d200c98776dbde"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO remove this branch once SamRecordClipper has been updated \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/umi/CodecConsensusCaller.scala"},"region":{"startLine":246}}}],"partialFingerprints":{"codehealthFindingId/v1":"556fb6ca9230a829b2fd5ab3fbba0fc7ba6ae136dd6666e17b15522a5e846fc5"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: could use a TreeSet to store the iterators, examine the head of each iterator, then pop the iterator with the min, \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala"},"region":{"startLine":73}}}],"partialFingerprints":{"codehealthFindingId/v1":"80a831523680c0395aa542e3966905f1ef813a72af9a00478ca2e9e2e97a5007"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO add subclasses for ALT and PEDIGREE lines \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/api/VcfHeader.scala"},"region":{"startLine":74}}}],"partialFingerprints":{"codehealthFindingId/v1":"077e74aee3ad6c4b2896cdcf648e541c209cc2c1b37618fc9ffdc97ac0f15fda"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: what does this need to have \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/api/Allele.scala"},"region":{"startLine":118}}}],"partialFingerprints":{"codehealthFindingId/v1":"d52832bb48ab19d1e377b31173e205b0f080f8e306e6d2a826a65bbf4075bf0c"}},{"ruleId":"D17","level":"warning","message":{"text":"HackComment: // Hack to allow reference by position without offset by 1 \u2014 a workaround marked in source: record what it is compensating for and what would allow its removal (the upstream fix, the API it is waiting on, the invariant it restores), so the next reader can judge whether it is still needed rather than rediscovering why it is there."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/test/scala/com/fulcrumgenomics/bam/ErrorRateByReadPositionTest.scala"},"region":{"startLine":297}}}],"partialFingerprints":{"codehealthFindingId/v1":"a7850e8e62649c0767cbbef0a8a221f6be42963bc0cc10596daaa94b46731085"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Consider creating more unit tests that vary the following metric fields \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/test/scala/com/fulcrumgenomics/umi/GroupReadsByUmiTest.scala"},"region":{"startLine":296}}}],"partialFingerprints":{"codehealthFindingId/v1":"cd1bebfd77b44e496181c528bd789fd235ec57bfc8e7ef2cd7993c259c9b4bb2"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: BUG!!! These variables are never passed down into the interval list. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/test/scala/com/fulcrumgenomics/vcf/AssessPhasingTest.scala"},"region":{"startLine":210}}}],"partialFingerprints":{"codehealthFindingId/v1":"0830bba885941073af45fbd29f0537dcea627a99a3d45468c982d28f7c74f90a"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: BUG!!! This is meant to be start and end, but that is not happening. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/test/scala/com/fulcrumgenomics/vcf/AssessPhasingTest.scala"},"region":{"startLine":213}}}],"partialFingerprints":{"codehealthFindingId/v1":"0538b6dc9536a61a8d3cc5bd1d3d7b887b458051745b2ab24731010c0ae3f53e"}},{"ruleId":"D20","level":"note","message":{"text":"No ADRs found: No ADRs found. No recognised ADR directory (\u0060docs/adr/\u0060, \u0060docs/decisions/\u0060, \u0060adr/\u0060, \u0060docs/rfcs/\u0060, an \u0060ADR0001/\u0060 folder, or their siblings) exists anywhere in this tree. What was searched, so you can tell an empty log from a search that missed one: every directory under the tree (build output, dependencies and VCS metadata excepted), for a document that is either any non-index page inside a recognised ADR directory, whatever its name and however deeply nested (\u0060docs/adr/use-postgres.md\u0060, \u0060docs/adr/2024/0001-x.md\u0060); or a file anywhere whose name is ADR-shaped (\u00600001-use-postgres.md\u0060, \u0060adr-012-caching.md\u0060); or, when neither turned anything up, a document carrying the decision-record signature (an \u0022Architecture Decision Record\u0022 heading, or Status / Context / Decision / Consequences as section headings). A decision log that clears none of these \u2014 unnumbered files outside any recognised directory, without those headings \u2014 is not seen by this check and this row is then wrong. If that is your case, say so rather than renaming anything; otherwise, consider recording architectural decisions in \u0060docs/adr/\u0060."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"d2bea044ff79d7d275f5a91a6e2f548586178eaf480274c33960ad020c854631"}},{"ruleId":"D26","level":"note","message":{"text":"Projects may be oversized for their cohesion: 1 of 1 project(s) overshoot their size bounds, lowering Project Cohesion to 0.0/10. The most over is \u0060(repository root)\u0060 (28018 LoC, 557 module-visible types across 23 directories). Review these for cohesion \u2014 draw the boundary inside the module first (group each responsibility into its own package or directory and keep the cross-boundary members non-public), since splitting a published package moves types between packages and breaks consumers."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"d5a94650dc74886a0f1f08eb9fb6775f1fc395279ef7e901c970c9d26f767a72"}},{"ruleId":"D28","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"3129f8757bb3b018cdf64476b44f42260a01185486c76fab600a8c1de45bfae9"},"properties":{"commitSha":"3711f2d7f7e51ae1ec175eddace474fe89dec85d"}},{"ruleId":"D28","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"76cd508ef39c52eca81f56a97e75c9c2dbba3cc568615c4eb417133236e999e1"},"properties":{"commitSha":"3711f2d7f7e51ae1ec175eddace474fe89dec85d"}},{"ruleId":"D28","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"ea3c5318f4d66634620d2fcce4da42b7a99f888f48c0d3688cf626ab2ad6192b"},"properties":{"commitSha":"3711f2d7f7e51ae1ec175eddace474fe89dec85d"}},{"ruleId":"D28","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"39928c4a43194a42a6292d6af6dee75eccbb945d5f89b0e36e9f5dae823641cf"},"properties":{"commitSha":"3711f2d7f7e51ae1ec175eddace474fe89dec85d"}},{"ruleId":"D28","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"3cdfd7beb31b791ae18dcb425e21eb157c842e7bbcd522cc330573c1a6538db1"}},{"ruleId":"D30","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"fb24589fac82866e1a453efba8f5edf5b570ecd947f2c4a8ff502f853afa1c85"},"properties":{"dependency":{"package":"log4j-core","version":"[2.26.0,)","advisory":"[GHSA redacted]","aliases":["[CVE redacted]","[CVE redacted]","[CVE redacted]","[GHSA redacted]","[GHSA redacted]"],"reachability":{"kind":"unknown"}}}},{"ruleId":"D30","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"200cf964a08e21372cb366c2dfb3daa6308635f7cf5e32258be6ed18e35e8b18"},"properties":{"dependency":{"package":"snappy-java","version":"[1.1.10.7,)","advisory":"[GHSA redacted]","aliases":["[CVE redacted]","[CVE redacted]","[CVE redacted]","[CVE redacted]","[GHSA redacted]","[GHSA redacted]","[GHSA redacted]"],"reachability":{"kind":"unknown"}}}},{"ruleId":"D34","level":"error","message":{"text":"Orphaned knowledge: No living knowledge remains for this large file \u2014 its last meaningful change has decayed away; if it breaks, no one currently understands it. Schedule a read-through / add characterisation tests before it bites."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/vcf/DownsampleVcf.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"059aa8647ba9cf00a16cbcba8e194035c8d690dd0533961ea0ae350d66c8b7c0"}},{"ruleId":"D34","level":"note","message":{"text":"Further orphaned files (smaller): 5 smaller file(s) also have no living knowledge \u2014 folded into the freshness score and metrics rather than raised one row each \u2014 most significant first: src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala, src/main/scala/com/fulcrumgenomics/bam/pileup/StreamingPileupBuilder.scala, src/main/scala/com/fulcrumgenomics/fasta/SortSequenceDictionary.scala, src/main/scala/com/fulcrumgenomics/bam/pileup/RandomAccessPileupBuilder.scala, src/main/scala/com/fulcrumgenomics/bam/pileup/Pileup.scala (6 orphaned of 137 analysed files in total, counted over production source files of roughly 2,400 bytes or more, excluding vendored, generated and example/demo trees and test files identified by path convention, largest first; 137 of the 150 production source files in this repository met that bar). Attach the read to the next change that touches one of them: have a second person review that change, and leave behind a short comment or test recording what the file is for, so the knowledge comes back at the cost of a change you were making anyway."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"ce861fd78f6935114d3a342cb90ad25870f984e1042954fcbbe27c0e23be3658"}},{"ruleId":"D34","level":"note","message":{"text":"Orphaned file: No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"b6537d10ac6a4265239c32f7d143d3a5628f24782847f98e9d2bcd694e90a302"}},{"ruleId":"D34","level":"note","message":{"text":"Orphaned file: No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/StreamingPileupBuilder.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"19ce6c179be8442cf10f7975729c7b2f1093881c11bf4f10bb9fa99a4e35ef43"}},{"ruleId":"D34","level":"note","message":{"text":"Orphaned file: No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/fasta/SortSequenceDictionary.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac3a1641e818ea3ac18d0f55f2e8a98ed2f8eac4bc1ddbe456f74cf9ac094dcf"}},{"ruleId":"D34","level":"note","message":{"text":"Orphaned file: No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/RandomAccessPileupBuilder.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"c88df470c003054db69979dcf5d9e9e1458e477d1cf1cb91e82fc33f58def565"}},{"ruleId":"D34","level":"note","message":{"text":"Orphaned file: No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/Pileup.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"2a2bc2447675888c62a6d9755fdb3d41dd892840072ca9eadcd9d9f61836d05a"}},{"ruleId":"D36","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"1b213f6eedd4b140d0bc37bdf1496f72811a643f34064f12518b32e9e83bcfc7"},"taxa":[{"id":"CICD-SEC-9","toolComponent":{"name":"OWASP Top 10 CI/CD Security Risks","guid":"3c9b2a6e-5d14-4f7b-8e02-6a1d9c4b7f35"}}]},{"ruleId":"D36","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"eb00976a698a5d68999b7ee6d27206fd374e916853e7ff1ead5eed42386f043f"},"taxa":[{"id":"CICD-SEC-9","toolComponent":{"name":"OWASP Top 10 CI/CD Security Risks","guid":"3c9b2a6e-5d14-4f7b-8e02-6a1d9c4b7f35"}}]},{"ruleId":"D36","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"9739ac06004000f598da4fd175a92f0d9f5c718b41d35f1b1657c1cae478bb8b"},"taxa":[{"id":"CICD-SEC-6","toolComponent":{"name":"OWASP Top 10 CI/CD Security Risks","guid":"3c9b2a6e-5d14-4f7b-8e02-6a1d9c4b7f35"}}]},{"ruleId":"D36","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"38b1591c6e4e89526239c8b59a0b613fb41e1dc0e5e9acd7a8373079a8a5de8f"},"taxa":[{"id":"CICD-SEC-6","toolComponent":{"name":"OWASP Top 10 CI/CD Security Risks","guid":"3c9b2a6e-5d14-4f7b-8e02-6a1d9c4b7f35"}}]},{"ruleId":"IC1","level":"note","message":{"text":"Disabled test: A test is skipped/ignored \u2014 coverage that looks present but never runs. Re-enable it or delete it so the green run means something."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/test/scala/com/fulcrumgenomics/alignment/AlignerTest.scala"},"region":{"startLine":565}}}],"partialFingerprints":{"codehealthFindingId/v1":"c0cf2f588b45c9b45d87c06a0b0b03fd71e8a46d5a21872d9699e532343cdb29"}},{"ruleId":"M2","level":"note","message":{"text":"No ADRs: No Architecture Decision Records found \u2014 no conventional ADR directory, no numbered \u0060NNNN-title\u0060 documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"670b3d6e36a756d63097d0dfbf90afd5fc761308800b9354894a07c3f4e4aa14"}},{"ruleId":"P3","level":"note","message":{"text":"No SAST: No static application security testing detected. For this repository\u0027s stack, add scalafix or scapegoat (or \u0060semgrep --config=auto\u0060, which runs on any language) as a CI step. What was searched, so you can tell an absence from a miss: the 12352 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge\u0027s web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen \u2014 if that is your case the row is wrong, and saying so is more useful than adding a second scanner."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"6e54424179c892f03ef2fd003130ac4bd43f39bbf3b1ca0a0143e25acb80ec87"}},{"ruleId":"X10","level":"note","message":{"text":"Duplicated predicate: \u0060in.header.getSortOrder != SortOrder.queryname \u0026\u0026 in.header.getGroupOrder != GroupOrder.query\u0060 appears character-identically in 2 files \u2014 src/main/scala/com/fulcrumgenomics/bam/FindSwitchbackReads.scala, src/main/scala/com/fulcrumgenomics/bam/SetMateInformation.scala. It is one line, so the duplication detector\u0027s token window never sees it; the copies drift when only one is corrected. Give the condition a name and one home."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/FindSwitchbackReads.scala"},"region":{"startLine":343}}}],"partialFingerprints":{"codehealthFindingId/v1":"b6408329e5b1c1d5a3e1c3860e97dc185608e28adada662e927c697fd1528d4b"}},{"ruleId":"X10","level":"note","message":{"text":"Duplicated predicate: \u0060rec.quals != null \u0026\u0026 rec.quals.length != 0\u0060 appears character-identically in 2 files \u2014 src/main/scala/com/fulcrumgenomics/bam/Bams.scala, src/main/scala/com/fulcrumgenomics/bam/TrimPrimers.scala. It is one line, so the duplication detector\u0027s token window never sees it; the copies drift when only one is corrected. Give the condition a name and one home."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/Bams.scala"},"region":{"startLine":482}}}],"partialFingerprints":{"codehealthFindingId/v1":"a25c555445ffd4c8d04fcecce267259d3b7a3b039d3048a0d4a6b1d82ad6d1a7"}},{"ruleId":"X10","level":"note","message":{"text":"Duplicated predicate: \u0060rec.refIndex == refIndex \u0026\u0026 rec.start \u003C= pos \u002B 1\u0060 appears character-identically in 2 files \u2014 src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala, src/main/scala/com/fulcrumgenomics/bam/pileup/StreamingPileupBuilder.scala. It is one line, so the duplication detector\u0027s token window never sees it; the copies drift when only one is corrected. Give the condition a name and one home."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala"},"region":{"startLine":202}}}],"partialFingerprints":{"codehealthFindingId/v1":"8dd4b011d4a93234a8ea9f4d319ed9660f5838fe8561e8ded47dba9f687f11d5"}},{"ruleId":"X10","level":"note","message":{"text":"Duplicated predicate: \u0060so == SamOrder.Unsorted || so == SamOrder.Unknown\u0060 appears character-identically in 2 files \u2014 src/main/scala/com/fulcrumgenomics/bam/api/SamWriter.scala, src/main/scala/com/fulcrumgenomics/testing/SamBuilder.scala. It is one line, so the duplication detector\u0027s token window never sees it; the copies drift when only one is corrected. Give the condition a name and one home."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/api/SamWriter.scala"},"region":{"startLine":83}}}],"partialFingerprints":{"codehealthFindingId/v1":"a5be559fda837fd3f5e9e9219ccb7a5a2d2d1ce41f44fbfd5ae18422e7ce1f3f"}},{"ruleId":"X18","level":"warning","message":{"text":"Disposable created and abandoned in the function that made it: \u0060Source.fromFile(\u2026)\u0060 opens something that has to be given back \u2014 a file descriptor, a socket, a directory handle \u2014 and its only use reads \u0060.getLines\u0060 through it and drops it, so this expression both creates the value and is the last place that can release it, and does not. Every call leaks one more open handle until the collector happens to reach it: \u0060Too many open files\u0060 under load, and on Windows a file that cannot be replaced or deleted while it is held. Open it with \u0060scala.util.Using.resource(Source.fromFile(\u2026)) { r =\u003E \u2026 }\u0060, which releases it on every path including a throw, or hold it and call \u0060.close()\u0060 in a \u0060finally\u0060."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/illumina/SampleSheet.scala"},"region":{"startLine":69}}}],"partialFingerprints":{"codehealthFindingId/v1":"ae2e6436dd85530c473a10b7767fe0045cbb46bd605d026fa44527717b0646b1"}},{"ruleId":"X3","level":"warning","message":{"text":"Swallowed exception (caught, then discarded): \u0060case _: Exception\u0060 takes every exception and records none of it \u2014 the body neither logs it, rethrows it, nor even names it, so the failure is discarded as completely as by an empty catch and only the substituted value survives. Log it through whatever this codebase already uses to report problems, narrow the catch to the exception this call can actually raise, or say in a comment on the catch why the failure genuinely cannot matter."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/cmdline/FgBioMain.scala"},"region":{"startLine":163}}}],"partialFingerprints":{"codehealthFindingId/v1":"bbff5ed8b6ec42841b4b77f0d7a4ec254b5519e1572cd47425693f2083dc5f9c"}},{"ruleId":"X3","level":"warning","message":{"text":"Swallowed exception (caught, then discarded): \u0060case _: Exception\u0060 takes every exception and records none of it \u2014 the body neither logs it, rethrows it, nor even names it, so the failure is discarded as completely as by an empty catch and only the substituted value survives. Log it through whatever this codebase already uses to report problems, narrow the catch to the exception this call can actually raise, or say in a comment on the catch why the failure genuinely cannot matter."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/util/Rscript.scala"},"region":{"startLine":50}}}],"partialFingerprints":{"codehealthFindingId/v1":"23b00c1e9688758747c85d736b0babcd6e018e6082af583db1551375cbfa0042"}},{"ruleId":"X5","level":"note","message":{"text":"Scala\u0027s null is not held to the type system everywhere: No build over this repository\u0027s 144 Scala product file(s) passes \u0060-Yexplicit-nulls\u0060, enables WartRemover\u0027s \u0060Null\u0060 wart or runs Scalafix\u0027s \u0060DisableSyntax.noNulls\u0060, so every reference type admits null and nothing reports a \u0060null\u0060 written into the code or returned from a Java API \u2014 the first one to reach a method call is a \u0060NullPointerException\u0060. \u0060Option\u0060 by convention is a habit no tool here holds the code to."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"23e7c3c6da50151f07723c64ca4f881fd5903e713d143161a7c0594ad7ba29cc"}},{"ruleId":"X7","level":"note","message":{"text":"Silent fallback default on parse failure: \u0060countOf\u0060 answers \u00600\u0060 when \u0060IllegalArgumentException\u0060 is thrown, with no log or throw \u2014 a malformed value silently becomes that default. Log the input or fail validation. If that constant is the correct answer rather than a stand-in for a value that could not be read, say so in a comment in the catch case or in the Scaladoc, and the row stops firing."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"src/main/scala/com/fulcrumgenomics/bam/ErrorRateByReadPosition.scala"},"region":{"startLine":234}}}],"partialFingerprints":{"codehealthFindingId/v1":"860f671f88b89aa037ac0c44936fef9218e8407d101102ce6366633dcece9ef0"}}],"taxonomies":[{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d","organization":"MITRE","informationUri":"https://cwe.mitre.org/","isComprehensive":false,"shortDescription":{"text":"The MITRE Common Weakness Enumeration (CWE)."},"taxa":[{"id":"CWE-1357","guid":"e4d2e772-757e-0a5c-bd7d-77052949d866","name":"Reliance on Insufficiently Trustworthy Component","shortDescription":{"text":"Reliance on Insufficiently Trustworthy Component"},"helpUri":"https://cwe.mitre.org/data/definitions/1357.html"},{"id":"CWE-1395","guid":"800e09e7-c11a-8654-9fa6-86f398995fed","name":"Dependency on Vulnerable Third-Party Component","shortDescription":{"text":"Dependency on Vulnerable Third-Party Component"},"helpUri":"https://cwe.mitre.org/data/definitions/1395.html"},{"id":"CWE-259","guid":"ae9ad959-fbb6-9d5e-892d-3dca66da0b69","name":"Use of Hard-coded Password","shortDescription":{"text":"Use of Hard-coded Password"},"helpUri":"https://cwe.mitre.org/data/definitions/259.html"},{"id":"CWE-494","guid":"b8a65e0d-e459-4a55-a931-fc1136482375","name":"Download of Code Without Integrity Check","shortDescription":{"text":"Download of Code Without Integrity Check"},"helpUri":"https://cwe.mitre.org/data/definitions/494.html"},{"id":"CWE-506","guid":"401d6455-56e3-0552-9a39-f77461673e3f","name":"Embedded Malicious Code","shortDescription":{"text":"Embedded Malicious Code"},"helpUri":"https://cwe.mitre.org/data/definitions/506.html"},{"id":"CWE-77","guid":"332c8ade-6612-9f56-a06b-d8d90b1a8750","name":"Improper Neutralization of Special Elements used in a Command (\u0027Command Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Special Elements used in a Command (\u0027Command Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/77.html"},{"id":"CWE-78","guid":"2e31ceaf-c7ae-2e5e-9661-cfb1362789cf","name":"Improper Neutralization of Special Elements used in an OS Command (\u0027OS Command Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Special Elements used in an OS Command (\u0027OS Command Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/78.html"},{"id":"CWE-79","guid":"fd45580b-e8c4-fc5e-8c2f-aa8fab0b4dbf","name":"Improper Neutralization of Input During Web Page Generation (\u0027Cross-site Scripting\u0027)","shortDescription":{"text":"Improper Neutralization of Input During Web Page Generation (\u0027Cross-site Scripting\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/79.html"},{"id":"CWE-798","guid":"5e8f057d-fee3-995a-a0cb-9fc5b0d174d1","name":"Use of Hard-coded Credentials","shortDescription":{"text":"Use of Hard-coded Credentials"},"helpUri":"https://cwe.mitre.org/data/definitions/798.html"},{"id":"CWE-89","guid":"6d08fdad-37eb-c150-bbf0-d7d946863407","name":"Improper Neutralization of Special Elements used in an SQL Command (\u0027SQL Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Special Elements used in an SQL Command (\u0027SQL Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/89.html"},{"id":"CWE-937","guid":"16f316ae-415c-b354-a59b-1f7905f756e9","name":"Using Components with Known Vulnerabilities","shortDescription":{"text":"Using Components with Known Vulnerabilities"},"helpUri":"https://cwe.mitre.org/data/definitions/937.html"},{"id":"CWE-94","guid":"75e7f50c-6c2f-dd52-bf40-bf6c52b861fd","name":"Improper Control of Generation of Code (\u0027Code Injection\u0027)","shortDescription":{"text":"Improper Control of Generation of Code (\u0027Code Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/94.html"}]},{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61","version":"2025","organization":"OWASP Foundation","informationUri":"https://top10.owasp.org/2025/","isComprehensive":false,"shortDescription":{"text":"The OWASP Top 10:2025 web application security risks."},"taxa":[{"id":"A03:2025","guid":"168e227c-7735-2e57-bc6e-997affe644c5","name":"Software Supply Chain Failures","shortDescription":{"text":"Software Supply Chain 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