Eric Banks df6499e58c Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int. ... For reads with high MQs (greater than max byte) the MQ was being treated as negative and failing the min MQ filter. Added unit test. Delivers PT#61567540.		2013-11-27 18:55:03 -05:00
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annotator	Improvements to the reference model pipeline.	2013-11-01 17:58:25 -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	Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int.	2013-11-27 18:55:03 -05:00
diagnostics	add unit tests	2013-10-04 11:44:07 -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	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00
haplotypecaller	Introducing the latest-and-greatest in genotyping: CalculatePosteriors.	2013-11-27 13:00:45 -05:00
indels	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -04:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	adding a check for the UNAVAILABLE case of GenotypeType in CountVariants	2013-08-29 17:27:00 -04:00
variantrecalibration	Remove org.apache.commons.collections.IteratorUtils dependency from the test suite	2013-08-21 19:44:02 -04:00
variantutils	Merged bug fix from Stable into Unstable	2013-10-10 14:31:33 -04:00