Brent Pedersen

I see. Thanks for the response. For that example, I also don't mind bitshifting myself. I do have a related question. I was just trying out wrapping htslib. The first...

> You've set up bindLib correctly, but you called hts_open with 1 arg instead of 2. Since Cyber currently has function overloading by number of params, it say's it's missing...

does your bam file have chromosomes with the "chr" prefix?

it does, but it's probably better to name it hts_nim_tools. I can change this if it simplifies things.

a VCF QC tool that takes a multi-sample VCF and finds big contiguous chunks where a sample has all missing genotypes could indicate that a processing chunk (e.g. from a...

These are good ideas--though maybe more than bite-sized. :) I'll be writing a pileup engine soonish. I like the idea of VCF-to-VCF comparison, but there are a lot of considerations...

@brainstorm what would it do that sambamba slice does not? I guess there could be an API-ish way to access uncompressed blocks.

I'll have a look. Not sure if htslib even exposes this--I think sambamba could do it because it has its own wrappers.

yes, if those are in the exposed api (in the header) files, then they can be added to hts_concat.h, if you or someone else wants to write an example or...

downloadable from here: http://dpv.cmg.med.keio.ac.jp/dpv-pub/variants at bottom of page.