fix(nanno): deal with contig names that include numbers and letters #390
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…limit to standard contigs
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Pull Request Overview
This PR fixes a bug in nanno by ensuring that contig names that include both numbers and letters (e.g. "chr22_KI270739v1_random") no longer cause a NumberFormatException by filtering out non-standard contigs.
- Updated unit tests for convertContigNameToInt to cover various contig naming conventions
- Refactored ChrPositionUtils.convertContigNameToInt to use an isDigits helper method and enhanced contig filtering logic in Annotate.java
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| qcommon/test/org/qcmg/common/util/ChrPositionUtilsTest.java | Added extensive unit tests for various contig naming patterns |
| qcommon/src/org/qcmg/common/util/ChrPositionUtils.java | Updated contig conversion logic with a new isDigits helper method |
| qannotate/src/au/edu/qimr/qannotate/nanno/Annotate.java | Added contig filtering based on a defined set of standard GRCh38 contigs |
newellf
approved these changes
May 15, 2025
Co-authored-by: Copilot <[email protected]>
Co-authored-by: Copilot <[email protected]>
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Description
Skip VCF records that are not in the standard list of contigs. Reason for this is that the annotation sources only supply data for the standard contigs.
Bug in nanno where contig name with numbers and letters (eg
chr22_KI270739v1_random) would cause aNumberFormatExceptionhas been fixed.Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Additional unit tests have been added, existing tests pass, code has been run on vcf that highlighted these issues and now completes succesfully.
Are WDL Updates Required?
n/a