Eric Banks 2c3c680eb7 Misc changes and cleanup from all previous commits in this push. ... 1. By default, do not include the UG CEU callset for assessment. 2. Updated md5s that are different now with all the HC changes.		2013-06-11 12:53:11 -04:00
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annotator	Refactor rsID and overlap detection in VariantOverlapAnnotator utility class	2013-06-10 15:51:13 -04:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Make BQSR calculateIsIndel robust to indel CIGARs are start/end of read	2013-05-31 13:58:37 -04:00
compression/reducereads	Fix error in merging code in HC	2013-05-31 16:29:29 -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	Refactor rsID and overlap detection in VariantOverlapAnnotator utility class	2013-06-10 15:51:13 -04:00
haplotypecaller	Misc changes and cleanup from all previous commits in this push.	2013-06-11 12:53:11 -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