Matt Shirley

As a comment about the test suite, I think the test discovery could be improved. After updating to the latest GEMINI I was told: `Run test suite with: cd /path/to/gemini/share/gemini...

I'll just put a +1 for this. Sorted BAM input is already a requirement, so this should be simple.

Wow thanks for the quick response! I’ll check file sizes after I get the kids in 🛌. Matt > On Dec 18, 2019, at 5:44 PM, Rob Patro wrote: >...

My file sizes are mostly the same: ``` -rw-r--r-- 1 shirlma2 shirlma2 697K Dec 17 14:25 complete_ref_lens.bin -rw-r--r-- 1 shirlma2 shirlma2 2.7G Dec 17 15:36 ctable.bin -rw-r--r-- 1 shirlma2 shirlma2...

I just reindexed my transcripts fasta using salmon v1.0 and still have the exact same error messages. Just to check, I also tested on a CentOS7 machine with a different...

Sounds good. Thanks again for the help tonight. I should point out that I posted my log with `--quiet` so the zero length transcript messages are missing. Looking here: https://github.com/COMBINE-lab/salmon/blob/ea80f3a12a1a6ccb871a92175eda0bf94d2b114f/include/ReadExperiment.hpp#L311-L320...

To explain what I'm working on (and maybe it's a terrible idea): 1. Decoy sequences are a good idea but it's kind of silly to have limited baits with mappings...

I have lots of comments when I get back to my computer but right now wanted to say I’m absolutely floored by your effort here and will test the new...

A couple of points in response to your comments above: - I wouldn't worry about supporting zero length FASTA entries during index construction, but it would be good to **raise...

Thanks for the v1.1.0-beta2 test build, @rob-p! I just tested in my environment and this release fixes the issues I was encountering. **Edit**: regarding the aux targets concept, I'd be...