選択できるのは25トピックまでです。 トピックは、先頭が英数字で、英数字とダッシュ('-')を使用した35文字以内のものにしてください。
 
 
 
 
Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' 10ヶ月前
contrib/biod Edited makefile, fixed import names 10ヶ月前
src/cbam Edited makefile, fixed import names 10ヶ月前
.gitignore Makefile 10ヶ月前
DEVELOPMENT.org Makefile 10ヶ月前
Documentation.md Add documentation 10ヶ月前
LICENSE.txt LICENSE + README 10ヶ月前
Makefile Makefile changes 10ヶ月前
README.org Plan 10ヶ月前
Writer_flow.pdf Writer flowchart 10ヶ月前
docs.org Test org-babel code execution 10ヶ月前
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structure.pdf Structure of CBAM file 10ヶ月前

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.