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Old 06-15-2012, 12:44 PM   #6
adaptivegenome
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Quote:
Originally Posted by tyxer View Post
Hi, genericforms:

I did not know bamtools has interface. Do you mean the API?
I only tried the command line functions.

Thank you

Yuxiang
Bamtools has an exceptional C++ API. Source and docs are here:
https://github.com/pezmaster31/bamtools

You can browse the API commands here in a pretty format:
http://pezmaster31.github.com/bamtools/annotated.html

This is the way to go if you are writing C++ code. You can also use samtools and picard tools for other programming interfaces. Furthermore if you just want to do some quick analysis and not write a complete software package, you can just use samtools or bamtools in command line mode to grab a region of the region (VIEW) and then as mentioned in earlier posts, just pipe to a PERL or PYTHON script.

Last edited by adaptivegenome; 06-15-2012 at 12:45 PM. Reason: added links to doc
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