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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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	New ReduceReads v2 with unclipped variant regions and soft-clipped bases	2012-06-08 14:58:31 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -04:00
testdata	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00