You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' 2 months ago
contrib/biod Edited makefile, fixed import names 2 months ago
src/cbam Edited makefile, fixed import names 2 months ago
.gitignore Makefile 2 months ago
DEVELOPMENT.org Makefile 2 months ago
Documentation.md Add documentation 2 months ago
LICENSE.txt LICENSE + README 2 months ago
Makefile Makefile changes 2 months ago
README.org Plan 2 months ago
Writer_flow.pdf Writer flowchart 2 months ago
docs.org Test org-babel code execution 2 months ago
dub.json init 2 months ago
layout.html Fixes 2 months ago
structure.pdf Structure of CBAM file 2 months ago

README.org

cBAM (column based BAM)

This repo contains the prototype for a column-based cBAM reader/writer which will (hopefully) outperform tools like sambamba. To make this happen the following steps are required:

  • Compile cbam binary with Makefile and no other dependency than BioD
  • Document design of cbam format in /doc/CBAM
  • Create cbam file from bam
  • Implement markdup on cbam
  • Write bam file from cbam

Usage


cbam view -f cbam < in.bam | cbam markdup | cbam view -f bam > markdup.bam

Installation

cBAM depends on

  • D compiler
  • Snappy shared lib

Debian

apt-get install ldc libphobos2-ldc-shared-dev libsnappy-dev

Development

See DEVELOPMENT

License

cBAM is published under a GPLv3 license. See LICENSE.txt.