Sliding Window refactor to account for indels

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* Sliding window now operates over the cigar string to handle indels correctly
* window slides first, then adds the read.
* fixed consensus generation at the end of a variable region
* Sliding reads no longer keep duplicate information of bases and qualities
* consensus read is now a valid sam record including RG information
* BaseIndex is no longer a private class of BaseCounts as it's a useful utility for other tools in the reduced reads
* Some optimizations to the code in general.

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This commit is contained in:

Mauricio Carneiro 2011-08-27 14:23:15 -04:00

parent 732f1f12b7

commit 32e74affe1

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