Updates parseSample to permit truncated sample values, containing#17
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carbocation wants to merge 1 commit into
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Updates parseSample to permit truncated sample values, containing#17carbocation wants to merge 1 commit into
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fewer entries than the FORMAT fields. This is permitted by the VCF 4.2 spec. It is present "in the wild" in VCFs that were produced by GATK from gVCFs.
brentp
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Mar 15, 2020
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Looks reasonable. Can you add a test-case (and possibly a test-vcf?)
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The demo VCF given at internationalgenome.org actually has an example of this (where a haplotype quality flag ["HQ"] is only given for phased calls, and one of the calls is not phased). Adding this as a note-to-self since I still haven't put together a test, initially due to lack of public example VCF. This solves that; now I just need to assemble it. |
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Updates parseSample to permit truncated sample values, containing fewer entries than the FORMAT fields. This is permitted by the VCF 4.2 spec. It is present "in the wild" in VCFs that were produced by GATK from gVCFs. Specifically, this fixes #16