• cBAM (column based BAM)
• Usage
• Installation
  • Debian
• Development
• License

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 /nickr/cBAM/src/branch/master/doc/CBAM.org

• 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 /nickr/cBAM/src/branch/master/DEVELOPMENT.org

License

cBAM is published under a GPLv3 license. See /nickr/cBAM/src/branch/master/LICENSE.txt.