James Bonfield

The original issue isn't something we can fix, so I'll close it here. As reported above, it's tracked elsewhere (with the people that can actually fix it, unlike us). The...

I have a PR incoming to fix this. It's https://github.com/samtools/samtools/blob/develop/bam_sort.c#L1968 (and one other place). 0xc0 is READ1 vs READ2. For ties we then need to fall back to primary vs...

For generating the header, there's currently no alternative. It has to compute the md5sum and CRAM mandates it unless we're using embedded references (which is an option of course, but...

See also #1569

Somewhat tardily, there is now a proposal for storing base modifications in SAM, BAM and CRAM: https://github.com/samtools/hts-specs/pull/418 Your thoughts on this would be appreciated. Have we forgotten something important? Is...

I'm not sure this is the correct place to comment, as Guppy is now the tool producing methylation and not Flappy, but I couldn't find Guppy on github. Anyway I've...

Thanks for the suggestion. Please do keep them coming, although right now this is rather a wish-list item and we haven't yet decided what priority the many competing ideas have...

The intention of samtools fastq is very much to reverse the alignment process. Ie to take an aligned file and reproduce something akin to the original instrument outputs so it...

The query names are used for read-pairing, but the names could be anything at all. It's just important that they match. Note SAM doesn't attach any meaning to specific suffixes...

Are you sure this isn't an issue of same input data (bar name), but different alignment output data? Some aligners are not stable and given the exact same input will...