Include VCF info field in v1 -> v2 conversion, improve handling of VCF filter fields in phenopacket builder

phenopackets / phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.

http://phenopackets.org/phenopacket-tools/stable/

GNU General Public License v3.0

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Include VCF info field in v1 -> v2 conversion, improve handling of VCF filter fields in phenopacket builder #185

Closed ielis closed 1 year ago

ielis commented 1 year ago

The PR fixes #184 and improves handling of the filter field when building a VcfRecord. The builder ensures that the final VcfRecord is not logically inconsistent and the filter field has one of the three following states:

empty - no filtering info
pass - filter==PASS
filtered - any sequence of ;-separated filter values