Melissa Gymrek

The main purpose of this PR is to make scripts fail when `subprocess.call(cmd, shell=True)` returns a non-zero exit status. In most cases it doesn't make sense for the scripts to...

Things like rRNA that can have millions of reads in a single locus currently fail when all of those reads are loaded into memory. We should at least detect when...

This is a longer term enhancement. I welcome discussion from others on this possible feature. The plan would be to also supply pybamview with a VCF, and then it would...

Use sphinx and host on read the docs

Make an hg38 reference

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We should build an hg38 reference and post to the website, and add scripts for the TRF step to the repo.

Fail to read read groups when PG is in header

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Pointed out by Isidro Cortes. When a @PG line is in the header, we report an error that no read groups are found "ERROR: No read groups found". This could...

Compiled from smaller scripts by @tfwillems and modified to adhere to required input format for lobSTR. This can probably be cleaned up in the future

Right now lobSTR re-annotates the library and sample information. But if these already exist and particularly if a BAM has multiple libraries in it, it could be useful for lobSTR...

I tried a fastq file with mixed upper/lower case and these failed to align until I tried a new fastq with all reads converted to upper case. We should probably...

We should make it clear that the new reference is much different than that included in the original lobSTR paper, and generally describe how we made it. We should add...