propagate PL values from reference bands

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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propagate PL values from reference bands #180

Closed mlin closed 4 years ago

mlin commented 4 years ago

If the output site is biallelic then the three PL values are effectively copied over.

If the output site is multiallelic, then the reference band's ref/non-ref (0/<*>) PL value is copied to the output PL entries for all ref/alt genotypes (triangular-numbered genotype indices). The hom-non-ref (<*>/<*>) PL value is copied to the remaining nonzero genotype indices.

More-thorough testing needed.

mlin commented 4 years ago

Should this be opt-in configurable?

coveralls commented 4 years ago

Coverage increased (+0.05%) to 93.381% when pulling 674a9cba28d0d8d014470973529d084c5b6e1f6a on mlin-ref-PL into 3ecfc2ffea8bcbf31e34f49574125679ba517caa on master.