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Nick Rozinsky ad2d51a73d Delete 'writer_flowchart.pdf' преди 10 месеца
contrib/biod Edited makefile, fixed import names преди 10 месеца
src/cbam Edited makefile, fixed import names преди 10 месеца
.gitignore Makefile преди 10 месеца Makefile преди 10 месеца Add documentation преди 10 месеца
LICENSE.txt LICENSE + README преди 10 месеца
Makefile Makefile changes преди 10 месеца Plan преди 10 месеца
Writer_flow.pdf Writer flowchart преди 10 месеца Test org-babel code execution преди 10 месеца
dub.json init преди 10 месеца
layout.html Fixes преди 10 месеца
structure.pdf Structure of CBAM file преди 10 месеца

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/

  • 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/


cBAM is published under a GPLv3 license. See /nickr/cBAM/src/branch/master/LICENSE.txt.