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andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
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set reference genome and annoation for `freyja extract` #170

Closed dwinter closed 1 year ago

dwinter commented 1 year ago

May thanks for this very useful tool!

We are now using the read analysis tools in freyja to go hunting for mutations of interest ,and ran into the issue that freyja extract is expecting the NC_045512.2. Would it be possible to make the reference genome and annotation optional arguments as theya re for covariants?

(Not a burning issue, at it's easiy enough to re-run the alignments)

dylanpilz commented 1 year ago

Hey,

Certainly! It's actually much simpler to pull the reference name directly from the input bam file as in covariants. I'll make this change to extract and filter and include it in the next release.

-Dylan