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Old 03-05-2012, 04:45 PM   #11
adaptivegenome
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Join Date: Nov 2009
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Quote:
Originally Posted by nilshomer View Post
I have been working on speeding up reading and writing within SAMtools by creating a multi-threaded block gzip reader and writer. I have an alpha version working. I would appreciate some feedback and testing, just don't use it for production systems yet. Thank-you!

http://github.com/nh13/samtools/tree/pbgzip

NB: I would be happy describe the implementation, and collaborate to get this into Picard too.
So are you saying you made a parallelized version of BZIP2? We have also been playing around with this. We parallelized the compression and decompression steps in the read/write functions of samtools for a local realignment tool we built.

I would love to learn more about what you are doing as I would hate to duplicate anything you are going to already do!
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