James Bonfield

+1 to this. I believe the transparent nature of reading *AM in htslib was one of the primary reasons that CRAM managed to get off the ground as it broke...

That's going back a bit in my memory! I had to hunt. There's scf_update which has a `-v` option to control the version number. It's a very simple program which...

It's the version you're writing too. From recollection the reading automatically detects the version and works either way. As an example: ``` @ seq4c[io_lib/build.x8...]; ./progs/scf_update -v 2 ~/work/mut_data/000906_11cR.scf _.scf;ls -l...

It builds, but there are no uses of it in the test harness. I can run it on the existing test data if I recreate the `tests/test.out/ce#sorted.full.cram` file using a...

I'll have a think. I think I already rely on things like awk and md5sum in the test harness, but not 100% sure so I should check. If they're portable...

I added a call to this in the test harness in a local branch containing this PR and rebased on top of some updates to master. I just added these...

You could also compare against static block-based arithmetic compression. I optimised one of those (unrolling and interleaving Eugene Shelwien's) just before Ryg posted his rANS, so then gave that the...

On Tue, Jan 19, 2016 at 08:51:38AM -0800, Sven-Eric Schelhorn wrote: > I was wondering if htslib/samtools support extraction of blocks of unaligned reads similar to what a bgzipped FASTQ...

I admit it's esoteric! But here's a worked example. ``` $ zcat _.cram.crai 19 18868 136639 7362 210 103725 19 155366 95912 111322 212 93967 19 251145 86228 205527 214...

This was implemented, but not in htslib. See io_lib's `cram_filter`. It's a bit clunky as it doesn't have an obvious way to tell you how many containers exist (other than...