Eric Banks 64d5bf650e Pulled out some hard-coded values from the read-threading and isActive code of the HC, and made them into a single argument. ... In unifying the arguments it was clear that the values were inconsistent throughout the code, so now there's a single value that is intended to be more liberal in what it allows in (in an attempt to increase sensitivity). Very little code actually changes here, but just about every md5 in the HC integration tests are different (as expected). Added another integration test for the new argument. To be used by David R to test his per-branch QC framework: does this commit make the HC look better against the KB?		2014-01-19 01:15:13 -05:00
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annotator	Pulled out some hard-coded values from the read-threading and isActive code of the HC, and made them into a single argument.	2014-01-19 01:15:13 -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	Pulled out some hard-coded values from the read-threading and isActive code of the HC, and made them into a single argument.	2014-01-19 01:15:13 -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