Matt Shirley

@KKPMW What you described would exactly fit my needs. I think that's the most generalized way to set up a matrix-oriented application of the 2x2 Fisher's test. I like the...

Thanks for looking into this! In fact p-values under the OR=1 null hypothesis would be useful for my project. I’d be glad to test out any implementation. > On Apr...

It looks like your GTF references gene models that are on patch contigs. You might be using the wrong genome assembly then (your gene models in the GTF need to...

Just in case it wasn't obvious, this was only partially a joke issue.

"Full run" and "fix this" urgency were in jest. Seriously though, just part of a run would be fine for tool test data.

Looks like @nickloman released some yesterday so maybe it could be linked from here?

It looks like there is no testing framework in poretools currently, so maybe once there is it could be split: 1. Unit tests that are for internal consistency and do...

As far as I know, BWA only accepts gzipped FASTA files during indexing, or as sequences to align. In either of these cases, BWA only needs to read the files...

I’ll point out that [pyfaidx](https://github.com/mdshw5/pyfaidx) supports BGZF compresses FASTA and the `faidx` script supports bed files as input. faidx -b ranges.bed /path/to/ref.fasta.gz