Matt Shirley

I'm using leafcutter with snakemake, which supports only python3. In any case it looks like python3 support is an easy addition to leafcutter, and should help drive new user adoption.

I jumped the gun on making this pull request. Will add more as I test against the python2.7 results.

Is this something that should be reviewed in mdshw5/simplesam as well?

No, simplesam only uses the CIGAR operations to inspect the alignment of the sequence, but does not interpret the match/mismatch operators. It seems like the SAM1.4 CIGAR operations don't completely...

You got me excited, since it really bothers me that we have two strings (CIGAR and MD) that basically represent the same information in a slightly different way.

We're experiencing similar issues with pysam, and as the author of pyfaidx please let me know if there's anything I could do to help. It's worth noting that pyfaidx.FastaRecord implements...

@guma44 I'll update this issue with progress and issues building a docker image. We should discuss how to integrate the container in Cromwell. I find [this in the Cromwell docs](https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#specifying-containers-in-your-workflow)...

It's not clear that the gene description will ever be in GTF files, as I can't find an example. Need to follow up and figure out the nature of this...

I think this is a great idea, but would also like to fall back on bundling a version of salmon that works with PISCES. Some of the older versions (<...

I'd just like to add my support for this feature. This is something I could use in a project I'm currently working on.