Jeremiah Wala

There are a few error modes that could pass through low quality events. The main one is DSCRD, which are events found only with discordant reads and not sequence assembly....

This is unusual behavior, but I do have a suggestion. There was an issue in the dedupe step that another user pointed out in issue #92, which I fixed in...

Hmm, that is an unusual situation with a gene listed on multiple chromosomes -- interesting catch. Happy to entertain a pull request if you have a better validation scheme. On...

Is this for germline or somatic rearrangement calling? If the latter, I would caution against converting to "DEL" "DUP" etc for reasons I can explain, and why I've never been...

Thanks! Glad it's usually fast. When it's not, I first suspect that there are a lot of discordant reads, which is causing it to do a lot of mate-region look-ups....

Thank you for the detailed report. I was able to recreate the issue, and see two things to address. The first is easy enough. fermi-lite actually deallocates the input sequences...

Hi Hannes, Thank you, this is an excellent point that I missed, and I agree that this should be fixed. I tried again all of the tests with the flags...

Hi Hannes, This was for the reading test. The "core" concept is from BamTools, and is the option to read in an alignment without decompressing all of the string data....

Latest benchmarks: 1. SeqLib + sequence expansion: 18.0s 2. SeqLib default: (as above): 13.6s 3. Jumping test: SeqLib 9.3s, SeqAn: 13.3s. 4. (adding in htslib test, copied from bam-perf-test): 9.46s...

Ok great, I think we're converging on what is going on! Thank you for the quick and courteous note about the benchmarking, and I'll reach out today to get that...