Nevar pievienot vairāk kā 25 tēmas Tēmai ir jāsākas ar burtu vai ciparu, tā var saturēt domu zīmes ('-') un var būt līdz 35 simboliem gara.
 
 
 
 
Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' pirms 10 mēnešiem
contrib/biod Edited makefile, fixed import names pirms 10 mēnešiem
src/cbam Edited makefile, fixed import names pirms 10 mēnešiem
.gitignore Makefile pirms 10 mēnešiem
DEVELOPMENT.org Makefile pirms 10 mēnešiem
Documentation.md Add documentation pirms 10 mēnešiem
LICENSE.txt LICENSE + README pirms 10 mēnešiem
Makefile Makefile changes pirms 10 mēnešiem
README.org Plan pirms 10 mēnešiem
Writer_flow.pdf Writer flowchart pirms 10 mēnešiem
docs.org Test org-babel code execution pirms 10 mēnešiem
dub.json init pirms 10 mēnešiem
layout.html Fixes pirms 10 mēnešiem
structure.pdf Structure of CBAM file pirms 10 mēnešiem

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.