SplitReads walker implementation (for AGBT talk)

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- walker simulates sequencing with different lengths to evaluate mapping/alignment biases relative to read length
   - split : splits reads n-ways generating 2^n reads for each read of the same length.
   - chop : chops the right end tail of the read creating 1 smaller read as if the sequencer stopped short.
   - mate information is preserved for chopped reads, and re-indexed for split reads so that each split still points at the corresponding split on the mate.
   - added systematic unit tests

GSATDG-23

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Mauricio Carneiro 2013-01-23 20:16:23 -07:00

parent a3b98daf1a

commit a4fbf9df1e

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