Improved handling of intersecting groups in SVStratify #9185
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…utput mode Add tests
epiercehoffman
approved these changes
May 23, 2025
| if (writer == null) { | ||
| throw new GATKException("Writer not found for group: " + stratum.getName()); | ||
| final List<String> stratumNames = new ArrayList<>(stratifications).stream().map(SVStratificationEngine.Stratum::getName).sorted().collect(Collectors.toUnmodifiableList()); | ||
| final VariantContext outputVariant = builder.attribute(GATKSVVCFConstants.STRATUM_INFO_KEY, stratumNames).make(); |
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It looks like the VCF header line for STRAT still has count=1, should it now be unbounded?
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Changes the behavior of SVStratify when a variant belongs to more than one stratification group:
STRATfield to a list type so that multiple groups can be listed--split-output--split-output, all groups are listed inSTRATrather than only the one corresponding to the output fileAlso adds tests and updates docs.