Enabled GVCF type filtering support in SelectVariants #7193
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ldgauthier
reviewed
Apr 12, 2021
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| final IntegrationTestSpec spec = new IntegrationTestSpec( | ||
| baseTestString(" --select-type-to-include SNP --ignore-non-ref-in-types ",testFile), | ||
| Collections.singletonList(getToolTestDataDir() + "expected/" + "testSelectVariants_VariantTypeSelectionForGVCF.vcf") |
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We've been trying to move away from brittle exact match integration tests, but I think that this is fine here since there are no opportunities for numerical changes.
ldgauthier
approved these changes
Apr 12, 2021
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@michaelgatzen is this ready to be merged? |
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I remember now why this was a draft for the longest time, and also probably why Travis failed - this was waiting for a release of htsjdk after samtools/htsjdk#1544, but I see that GATK master is using 3.0.1, which does include that htsjdk PR. It's probably still a good idea to run Travis |
- Added optional argument `--ignore-non-ref-in-types` to support correct handling of VariantContexts that contain a NON_REF allele - Default behavior does not change - Note that this only enables correct handling of GVCF input. The filtered output files are VCF (not GVCF) files, since reference blocks are not extended when a variant is filtered out - Added integration test
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Dependent on HTSJDK release after samtools/htsjdk#1544
Fixes #7111
--ignore-non-ref-in-typesto support correct handling of VariantContexts that contain a NON_REF allele