James Bonfield

> I also tried @jkbonfield's `samtools view -c` test and see nearly identical RAM utilization. I haven't yet tried iterating through many regions. Do you mean that samtools view -c...

Thanks for the clarification. What htslib calls does Manta make? Is it a pure open and stream through the data set work-flow? Is it opening and closing many times? Opening...

To double check, I just tried samtools view on a local CRAM file with and without the `@HD` header with 20 ranges, using valgrind, and it found no leaks. The...

_**analysis of schema types.**_ Identifiers - read groups, fragment names, etc, have no regexp associated with them. This means sooner or later people will start putting unicode in names or...

Agreed. While it could almost certainly be tightened up, that's more from a strictly-speaking stance rather than a lack of clarity in what the intention is for encodings. Regarding line...

The SAM header lines in BAM I was assuming should always be complete and ending in a newline, but looking at the SAM spec the regexp is per-line with nothing...

I accept that it can be hard to directly compare figures between different manufacturers, as they may not be calibrated, but the meaning of the Phred score is defined and...

The problem with base calling software is they typically output in FASTQ, which has no real concept of meta-data and headers. Consequentially the downstream processes that create SAM et al...

Absolutely that's the right thing to do where possible. There are certainly a few useful utility functions in samtools which could be added to htslib. Reverse complementing sequences, some argument...

I quite like the idea of being able to use VCF/BCF as a list of locations. It makes it more like the unix "join" command. Meanwhile, have you looked into...