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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/

  • Create cbam file from bam

  • Implement markdup on cbam

  • Write bam file from cbam


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


cBAM depends on

  • D compiler

  • Snappy shared lib


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


See /nickr/cBAM/src/branch/master/


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