Michael McCowan c3a933ce84 Adaptations to accomodate Tribble API changes, comprising mostly of the following. ... * Refactoring implementations of readHeader(LineReader) -> readActualHeader(LineIterator), including nullary implementations where applicable. * Galvanizing fo generic types. * Test fixups, mostly to pass around LineIterators instead of LineReaders. * New rev of tribble, which incorporates a fix that addresses a problem with TribbleIndexedFeatureReader reading a header twice in some instances. * New rev of sam, to make AbstractIterator visible (was moved from picard -> sam in Tribble API refactor).		2013-08-19 15:52:47 -04:00
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annotator	moved SnpEffUtilUnitTest to public tree	2013-07-30 17:51:40 -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	Two reduce reads updates/fixes:	2013-08-01 14:34:59 -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	Added onlyEmitSamples argument to UnifiedGenotyper	2013-08-09 11:00:15 -04:00
haplotypecaller	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
indels	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -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	Adding mode to VQSR to not output variant records that are filtered out after applying the recalibration. Necessary for 1000G calling.	2013-08-12 11:22:59 -04:00
variantutils	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00