James Bonfield

This doesn't seem to be generating much traffic, so I assume there is little appetite for it. I do need to get something though for base modifications, and that in...

I decided it can largely be done with extra options to the existing mpileup that cull some of the more problematic parsing features. So see https://github.com/samtools/samtools/pull/1311 for the PR that...

Checking the source code, this is deliberate. I think it is questionable behaviour as it is assuming all reads are present in the file. The pair flag indicates a paired-end...

Apologies I've been doing other things and forgot about this. However I still don't entirely understand the reason why fixmates is not run once, after alignments instead of trying to...

Duh I just noticed this too late. It may be the same bug I just fixed in the samtools version: https://github.com/samtools/samtools/pull/428

I just stumbled across this having the same issue. In my case I was just evaluating abra2 on a small section of GIAB data aligned against GRCh38. Producing a new...

It's possible to reheader BAMs without decompressing and recompressing all the BAM records. Once the header is done it's basically a read/write loop. Lots of I/O, but computationally quick. In...

Agreed with John above. It's probably fair to say however that the samtools and bcftools configure scripts ought to check specific versions better, and we should document the minimum htslib...

I'm not disagreeing that full symbol versioning wouldn't be a nice thing, but it's alsot quite a bit of work to maintain and there are risks there with accidents in...

Thanks for the clarification, but I still don't really understand how it changes anything. The package names in Debian may be libhts3 and libhts4, but the packages still have version...