monarch-initiative / pheval

A framework for empirical evaluation of phenotype matching and prioritisation
https://monarch-initiative.github.io/pheval/
Apache License 2.0
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Handle IndexError for spiking variants into a VCF #321

Closed yaseminbridges closed 5 months ago

yaseminbridges commented 6 months ago

If a variant entry position cannot be found for spiking a variant into a template VCF an Index error is thrown. For example, if the phenopacket has a variant on chrX, and there are no records of chrX variants in the VCF, then the index error is thrown. To overcome this, just add the variant to the end of the file and write a logger warning