James Bonfield

rans_static. rANS coder (derived from https://github.com/rygorous/ryg_rans)

io_lib. Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.

crumble. Exploration of controlled loss of quality values for compressing CRAM files

fqzcomp. Fastq compression tool

qpg. Pangenome explorations

fqzcomp5. C

htslib. C library for high-throughput sequencing data formats

samtools. Samtools with CRAM support (inherited from staden package io_lib).

htslib_benchmark. Benchmarking of htslib and other tools

io_trace. Summarises strace output

htscodecs. Custom compression for CRAM and others.

qual_smooth. C

mpeg_misc. Miscellaneous scripts and code for working on the MPEG genome-compression AHG

bcftools. This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

sam_realigner. Realigns SAM/BAM/CRAM files to fix pairwise vs multiple alignment issues.

gdcc. C