Eric Banks 9e858270d7 Moving this test up one level to where it actually belongs.		2014-01-19 02:33:11 -05:00
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annotator	Moving this test up one level to where it actually belongs.	2014-01-19 02:33:11 -05:00
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	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
haplotypecaller	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
indels	Added in a check for what would be an empty allele after trimming.	2014-01-15 11:04:19 -05:00
phasing	Add documentation for RBP, and also update the MD5 for the tests now that the output uses HP tags instead of '|', which is now reserved for trio-based phasing	2014-01-03 12:04:47 -05:00
rnaseq	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
simulatereads	Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF.	2014-01-15 13:49:31 -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
WalkerTestIntegrationTest.java	Moving this test up one level to where it actually belongs.	2014-01-19 02:33:11 -05:00