Ryan Poplin a1596791af Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-04-20 14:03:04 -04:00
..
CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
activeregionqc	Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).	2012-04-20 14:02:55 -04:00
annotator	Updating integration tests now that standard annotations support multiple alleles	2012-02-27 11:32:26 -05:00
beagle	Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)	2012-01-23 08:25:34 -05:00
bqsr	BQSR bug triage #3	2012-04-19 17:31:04 -04:00
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	GATKReport v1.0	2012-03-12 23:09:19 -04:00
diffengine	Fixing MD5's (new GATKReport header was missing from old md5's)	2012-03-19 15:28:45 -04:00
fasta	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
filters	Again, fixing the add call when we really mean replace	2011-11-21 19:15:56 -05:00
genotyper	My changes	2012-04-19 12:45:18 -04:00
indels	Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there.	2012-03-30 10:33:30 -04:00
phasing	Added respectPhaseInInput flag to RBP and integration tests	2012-03-22 17:40:21 -04:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
validation	Added integration test for ValidationSiteSelector, correct MD5's	2012-03-26 16:39:55 -04:00
varianteval	AC strat now checks if evals will be merged before throwing an error on multiple eval files.	2012-04-19 16:08:55 -04:00
variantrecalibration	Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls	2012-04-20 10:58:34 -04:00
variantutils	Final update for VE. VCFStreaming wasn't yet updated	2012-03-30 21:52:01 -04:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
FlagStatIntegrationTest.java	Adding integration test for Flag Stat	2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsUnitTest.java	Better location for the downsampling of reads in PrintReads	2012-01-14 14:06:09 -05:00