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Old 12-21-2011, 12:04 PM   #8
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 701
Default Single End bam to fastq ?

There's actually faster ways to do it, a hash table implementation I did was 5x faster, but had a fixed amount of memory. I just wanted something simple and guaranteed to work on about any system (including the 4GB nodes on biowulf at NIH) and would run fast enough that I didn't lose focus. The implementation above uses heap for unmatched pairs and so uses very little memory on a proper ("strict"?) paired end bam. Soon as the pair is matched, the node is deleted and the AVL tree is rebalanced. The pieces are there for a single end implementation, just need to cut some code out. I'll see if can do it; check back tomorrow. Everybody's welcome to do whatever they want with the code.
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