Eric Banks a5a68c09fa Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads. ... The problem ultimately was that ReadUtils.readStartsWithInsertion() ignores leading hard/softclips, but ReduceReads does not. So I refactored that method to include a boolean argument as to whether or not clips should be ignored. Also rebased so that return type is no longer a Pair. Added unit test to cover this situation.		2013-05-29 16:41:01 -04:00
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annotator	Update expected test output for Java 7	2013-05-01 16:18:01 -04:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Trivial BQSR bug fixes and improvement	2013-04-11 17:08:35 -04:00
compression/reducereads	Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.	2013-05-29 16:41:01 -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	Bugfix for GGA mode in UG silently ignoring indels	2013-05-24 13:47:26 -04:00
haplotypecaller	Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage	2013-05-29 12:07:12 -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