Chris Norman

FWIW, I went through the same cycle recently when I started to experiment with rust in genomics - I started with noodles, but abandoned it for the same reason.

@mjhipp Thanks for taking a stab at this. While it does fix the duplicate line problem, it changes current behavior in a way that we should at least think about....

After further discussing this internally and thinking more about it, I'm inclined to wait for a more complete fix to VCFHeader and address the numerous issues all at once rather...

I'd love to see that code removed - its a pretty awkward way to do the order validation anyway. I'd prefer to see it done as part of https://github.com/samtools/htsjdk/pull/1581 though...

Hi @d-cameron It looks like this is a couple of months behind master - can you rebase on current master before we start reviewing ? Thanks.

@d-cameron VCF 4.4 itself was not included in the deliverables for the grant, but its exactly the kind of thing we hope the grant-funded work will more readily enable. The...

@clintval Stable sounds good to me, but @lbergelson who is out on vacation really needs to weigh in (I'm not actually a maintainer).

Both samtools and sra have these caches, and although I see the value, I vaguely recall having been surprised by both of them in the past, so I'm luke warm...

@jmthibault79 Interesting - I actually meant to ask about this issue (external block content IDs of 0) when I was reviewing the encoding refactor PR, since I noticed there are...

There are definitely some CRAM test files floating around in both htsjdk and GATK that violate this (that is, that have external blocks with content ID=0), and in some cases...