Mauricio Carneiro 4aad7e23ef New ReduceReads v2 with unclipped variant regions and soft-clipped bases ... * Re-wrote the sliding window approach to allow the variant region not to clip the reads that overlap it. * Updated consensus to include only reads that were not passed on by the variant region, header counts are updated on the fly to avoid recompute * Added soft clipped bases to ReduceReads analysis by unclipping high quality soft-clips then re-clipping after reduce reads * Updated all integration tests		2012-06-08 14:58:31 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	New ReduceReads v2 with unclipped variant regions and soft-clipped bases	2012-06-08 14:58:31 -04:00
test	Bug fix in VQSR so that the VCF index will be created for the recalFile.	2012-06-08 11:51:28 -04:00