Implementation of CRAM 3.1 codecs. #1714
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…safe, precompile the name Tok regex, eliminate unnecessary code.
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Hello. Thank you very much for this PR! I learned this fix is critical for an IGV upgrade to support CRAM v3.1, which is very important to our projects. I am wondering if there’s an estimated timeline for merging. Much appreciated! |
…ns, fix the read name separator.
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@jerryliu2005 This branch is nearly done, but there are a few TODOs left, plus I want to do some more large-scale round trip testing. Those should get done over the next couple of weeks. However, this branch doesn't actually turn on CRAM 3.1 support - I have a separate, smaller branch for that which I'm using for testing. Once those are merged, we'll need to do an htsjdk release, and then IGV can upgrade. I'd hope/expect that all to happen in the Jan/Feb timeframe. |
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Hi @cmnbroad, thanks very much for the info! I will let the team know about the rough timeframe to be ready :) |
This is a squashed and rebased branch containing all of the changes from Yash's CRAM 3.1 codec branches. Draft until I get all of the issues resolved. Replacement for #1618, 1644, 1663 and 1704.