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contrib/biod | 1 year ago | |
src/cbam | 1 year ago | |
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DEVELOPMENT.org | 1 year ago | |
LICENSE.txt | 1 year ago | |
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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 /pjotrp/cBAM/src/branch/master/doc/CBAM.org
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 /pjotrp/cBAM/src/branch/master/DEVELOPMENT.org
cBAM is published under a GPLv3 license. See /pjotrp/cBAM/src/branch/master/LICENSE.txt.