Eric Banks c133909d32 Fixed edge condition in the realigner where a realigned read can sometimes get partially aligned off the end of the contig. ... Now we ignore such reads (which is much easier than trying to figure out when to soft-clip). Added unit test.		2014-01-08 00:37:28 -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 GC Content to DiagnoseTargets	2013-12-03 23:04:40 -05:00
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	Fixed up edge condition for clipping long reads in the HMM.	2014-01-01 19:05:09 -05:00
haplotypecaller	Fixed issue > 0 log likelihoods using GraphBased likelihood engine reported by Mauricio	2013-12-13 11:19:57 -05:00
indels	Fixed edge condition in the realigner where a realigned read can sometimes get partially aligned off the end of the contig.	2014-01-08 00:37:28 -05:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
rnaseq	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
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	Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file.	2014-01-02 14:46:04 -05:00
variantutils	Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.	2013-12-31 12:07:56 -05:00