fix(nanno): guard against mismatched array lengths in extractFieldsFromRecord#401
Merged
holmeso merged 2 commits intonanno_multi_genefrom Feb 27, 2026
Merged
fix(nanno): guard against mismatched array lengths in extractFieldsFromRecord#401holmeso merged 2 commits intonanno_multi_genefrom
holmeso merged 2 commits intonanno_multi_genefrom
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Co-authored-by: holmeso <7066552+holmeso@users.noreply.github.com>
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[WIP] WIP to address review feedback on pull request #400
fix(nanno): guard against mismatched array lengths in extractFieldsFromRecord
Feb 27, 2026
holmeso
approved these changes
Feb 27, 2026
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extractFieldsFromRecorditerated overfieldNames.lengthwhile indexing intofieldPositions[i], causingArrayIndexOutOfBoundsExceptionwhen the two arrays had different lengths.Changes
AnnotationSourceTSV.java: Change loop bound fromfieldNames.lengthtoMath.min(fieldNames.length, fieldPositions.length), safely processing only the overlapping entries.AnnotationSourceTSVTest.java: Add test cases for both mismatch directions —fieldNameslonger thanfieldPositionsand vice versa.Type of change
How Has This Been Tested?
AnnotationSourceTSVTest.extractFieldsFromRecord()covering both mismatch directions (more names than positions, more positions than names).Are WDL Updates Required?
No.
Checklist:
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