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' 10 kuukautta sitten
contrib/biod Edited makefile, fixed import names 11 kuukautta sitten
src/cbam Edited makefile, fixed import names 11 kuukautta sitten
.gitignore Makefile 11 kuukautta sitten Makefile 11 kuukautta sitten Add documentation 10 kuukautta sitten
LICENSE.txt LICENSE + README 11 kuukautta sitten
Makefile Makefile changes 10 kuukautta sitten Plan 11 kuukautta sitten
Writer_flow.pdf Writer flowchart 10 kuukautta sitten Test org-babel code execution 10 kuukautta sitten
dub.json init 11 kuukautta sitten
layout.html Fixes 10 kuukautta sitten
structure.pdf Structure of CBAM file 10 kuukautta sitten

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.