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contrib/biod | 1 year ago | |
src/cbam | 1 year ago | |
.gitignore | 1 year ago | |
DEVELOPMENT.org | 1 year ago | |
Documentation.md | 1 year ago | |
LICENSE.txt | 1 year ago | |
Makefile | 1 year ago | |
README.org | 1 year ago | |
Writer_flow.pdf | 1 year ago | |
docs.org | 1 year ago | |
dub.json | 1 year ago | |
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structure.pdf | 1 year ago |
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
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 /nickr/cBAM/src/branch/master/DEVELOPMENT.org
cBAM is published under a GPLv3 license. See /nickr/cBAM/src/branch/master/LICENSE.txt.