WardDeb
commented
4 months ago Hey Ward, what is the reason for keeping the untagged bam files coming out of the aligner? What do you think these would be useful for that other bam files that are kept would not provide?
Good point, I wasn't really aware we keep (two versions even) of the allele_flagged bam files. The only difference would be unaligned reads.. I've reverted the back to temping the untagged bamfiles.
Closes #989. Specifying the NMaskedIndex as the index name instead of an actual file resulted in the weird recursive wildcards issue. I don't understand the exact cause for it, though. I've updated the parser help to avoid confusion in the future.
I also un-temped the non-phased bams, as these can actually be useful. It would add a substantial disk footprint to the analyses folders but I'd leave that for the end-users.