Rory Kirchner

Join forces?

1

I'd be happy to deprecate clojupyter and work on clj-jupyter together. I looked at your code and you are a way better programmer than I am-- I'd learn a ton...

Handle biological replicates automatically

4

Hi Yarden, What about something like this: http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1318514284 for a tack on module at the end to handle biological replicates for calling the event-level differential splicing? I think you might...

Add python shebang to the top

10

Hey Yarden, Since this gets installed as a script I put the business up top to let it get executed.

Hi everyone, Hope all is well. The other flag-only options don't have a short option, and the -u option wasn't working so I swapped it to be more like the...

Show homozygous reference samples in the --show-samples and --show-families queries

4

Hi folks, What do you think about adding a flag or changing the behavior of `--show-samples` and `--show-families` to show the homozygous reference samples in addition to the variant_samples and...

pizzly missing a fusion from SRR1659964

14

Hi Pall, Thanks for making pizzly. I've been working on adding support for it and some other fast fusion callers to bcbio and have been seeing if I can figure...

Update README with gene collapsing and insert size commands.

4

Thanks, this pull request does two things. It updates the documentation to add the last step to collapse down to the gene level fusion calls. It also renames the two...

This isn't a bug, but would be useful to add to the documentation: GTF files need to be sorted in gene->transcript->exon order or else pizzly segfaults when making the index....

segfault on empty reads

10

Hi @najoshi, I'm using sickle to clean up some trimming with cutadapt and some of the reads coming from cutadapt can have length zero, which causes sickle to segfault. I...