32e74affe1
* 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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| settings | ||
| LICENSE | ||
| build.xml | ||
| ivy.xml | ||