Get refname from input bam for extract/filter

andersen-lab / Freyja

Depth-weighted De-Mixing

BSD 2-Clause "Simplified" License

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Closed dylanpilz closed 11 months ago

dylanpilz commented 11 months ago

As with covariants, use pysam.AlignmentFile.get_reference_name() to pull reference name instead of a user-specified parameter for extract and filter.
Resolves #170