Você não pode selecionar mais de 25 tópicos Os tópicos devem começar com uma letra ou um número, podem incluir traços ('-') e podem ter até 35 caracteres.
 
 
 
 
Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' 10 meses atrás
contrib/biod Edited makefile, fixed import names 10 meses atrás
src/cbam Edited makefile, fixed import names 10 meses atrás
.gitignore Makefile 10 meses atrás
DEVELOPMENT.org Makefile 10 meses atrás
Documentation.md Add documentation 10 meses atrás
LICENSE.txt LICENSE + README 10 meses atrás
Makefile Makefile changes 10 meses atrás
README.org Plan 10 meses atrás
Writer_flow.pdf Writer flowchart 10 meses atrás
docs.org Test org-babel code execution 10 meses atrás
dub.json init 10 meses atrás
layout.html Fixes 10 meses atrás
structure.pdf Structure of CBAM file 10 meses atrás

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.