Eric Banks ba531bd5e6 Fixing the 'header is negative' problem in Reduce Reads... again. ... Previous fixes and tests only covered trailing soft-clips. Now that up front hard-clipping is working properly though, we were failing on those in the tool. Added a patch for this as well as a separate test independent of the soft-clips to make sure that it's working properly.		2013-07-18 13:56:46 -04:00
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annotator	Fixes to several of the annotations for reduced reads (and other issues).	2013-06-16 01:18:20 -04:00
beagle	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
bqsr	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
compression/reducereads	Fixing the 'header is negative' problem in Reduce Reads... again.	2013-07-18 13:56:46 -04:00
diagnostics	Update MD5s and the Diagnose Target scala script	2013-05-13 12:06:17 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Better GATK version and command line output	2013-06-20 11:19:13 -04:00
haplotypecaller	Adding new pruning parameter to ReadThreadingAssembler	2013-06-17 16:46:40 -04:00
indels	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -04:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Update MD5s for VQSR header change	2013-04-16 11:45:45 -04:00
variantutils	CombineVariants no longer adds PASS to unfiltered records	2013-05-20 16:53:51 -04:00