Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updates parseSample to permit truncated sample values, containing #17

Open
wants to merge 1 commit into
base: master
Choose a base branch
from

Conversation

carbocation
Copy link

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

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.
@coveralls
Copy link

Coverage Status

Coverage decreased (-0.1%) to 66.968% when pulling d5dc8a6 on carbocation:feature/permit-shorter-sample-filters into 654ed2e on brentp:master.

Copy link
Owner

@brentp brentp left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks reasonable. Can you add a test-case (and possibly a test-vcf?)

@carbocation
Copy link
Author

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

vcfgo stricter than VCF spec in terms of sample filters
3 participants