Sometimes we may want to include "partially-mapped reads" in the alignment—for example, if the contig to which we are aligning these reads is incomplete for some reason.
The --no-rm-tmp-bam flag already serves this purpose: since the temporary BAMs (before filtering, after OSA filtering, and after OSA + PM filtering) are not deleted, the user can just use the "after OSA filtering" BAM in downstream analyses. However, it would be nice to avoid running PM filtering in the first place if it is not necessary.
So maybe we could add a flag option like --pm-filter/--no-pm-filter, or something? Where if --no-pm-filter is passed, we don't run PM filtering at all. Hmm -- I guess in this case we should use the same BAM names as usual, for the sake of clarity (so the final output BAM in this case would be sorted-osa-filtered.bam).
Sometimes we may want to include "partially-mapped reads" in the alignment—for example, if the contig to which we are aligning these reads is incomplete for some reason.
The
--no-rm-tmp-bamflag already serves this purpose: since the temporary BAMs (before filtering, after OSA filtering, and after OSA + PM filtering) are not deleted, the user can just use the "after OSA filtering" BAM in downstream analyses. However, it would be nice to avoid running PM filtering in the first place if it is not necessary.So maybe we could add a flag option like
--pm-filter/--no-pm-filter, or something? Where if--no-pm-filteris passed, we don't run PM filtering at all. Hmm -- I guess in this case we should use the same BAM names as usual, for the sake of clarity (so the final output BAM in this case would besorted-osa-filtered.bam).