Add Bfx.validate_bam

Open tavinathanson opened this issue 8 years ago • 2 comments

We want to ensure that, for example, failed runs of bwa-mem don't produce incomplete BAMs that might end up being processed downstream.

I'm not clear if I ran into this or whether this is a real concern, but there's a chance that I did and it is?

cc @ihodes @julia326

May 02 '17 20:05 tavinathanson

My guess is the cleanup node of bwa-mem was killed before it could rm the truncated BAM, but this tool would be nice to have anyway.

May 02 '17 20:05 ihodes

Another thing we can do, is make bwa-mem (or any tool) write to a tmp-file and do a rename at the end of the job.

May 02 '17 21:05 smondet