Tim Fennell

@zaeleus Thanks so much for the response. I'm sure that both myself and @sstadick would be happy to help if there is a way for us to do. @sstadick is...

I would also suggest (and am curious if others on this thread agree/disagree) that a solution that more or less maintained performance for BAM but reduced performance a bit for...

I think the real challenge here is how to control the level of thread creation, and how to handle situations where you are writing many BAM files (e.g. think of...

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@SilinPavel Thanks for doing this. I'll do a full review later but wanted to share some thoughts up front: 1. I'm surprised at the gains you see in SortSam. I...

Yeah, I thought you might have a reaction like that @lbergelson. My primary concern at this point is that I just want to be able to read Octopus VCFs without...

@jmarshall The same problem exists either way - if you use either @dancooke's representation or the standard `*` allele. I.e. if you have a deletion that spans a SNP variant,...

@lbergelson no worries - I wasn't taking this as 100% blocked, but rather figured it was useful to try and push the spec discussion forward some because it would be...

@yfarjoun & @ktibbett Could I request that you guys take a look at this PR please? Particularly it would be good, prior to merging, to ensure that this change won't...

@yfarjoun I've rebased and fixed conflicts, but am still getting test failures which I don't have time to debug right now.