Closed ricomnl closed 1 year ago
@sbooeshaghi @Lioscro this would be a useful addition IMO because BAM files are required for downstream tasks like genetic demultiplexing. Right now, one would have to use cellranger to get bam files. In addition, the PR would solve this previous issue https://github.com/pachterlab/kb_python/issues/147
@ricomnl I am the person currently making major upgrades to and maintaining kallisto. Thanks for the pull request. I have several updates I need to make first but I will try to merge this pull request when I can. Don't worry -- it's on my radar.
As long as the commands printed from --dry-run
looks reasonable, the changes lgtm.
@Lioscro all looks good to me; feel free to merge
kallisto bus
has the following optional options:This PR adds parameters to
kb count
so that one can use the--genomebam
flag as well as a gtf file and optionally a chromosomes file to output a .bam file. A test is added to make sure the functionality works as intended.