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Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' 2 years ago
contrib/biod Edited makefile, fixed import names 2 years ago
src/cbam Edited makefile, fixed import names 2 years ago
.gitignore Makefile 2 years ago
DEVELOPMENT.org Makefile 2 years ago
Documentation.md Add documentation 2 years ago
LICENSE.txt LICENSE + README 2 years ago
Makefile Makefile changes 2 years ago
README.org Plan 2 years ago
Writer_flow.pdf Writer flowchart 2 years ago
docs.org Test org-babel code execution 2 years ago
dub.json init 2 years ago
layout.html Fixes 2 years ago
structure.pdf Structure of CBAM file 2 years 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 /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.