Eric Banks 61a3dfae24 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2011-10-06 15:58:04 -04:00
..
CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers.	2011-09-23 16:06:52 -04:00
beagle	Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf	2011-09-13 16:57:37 -04:00
coverage	Updating MD5s	2011-10-04 15:54:45 -07:00
diffengine	Spelling fix requires md5 updates	2011-08-26 07:40:44 -04:00
fasta	More updates to be consistent with the new rod syntax.	2011-08-09 10:11:37 -04:00
filters	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
genotyper	Updating UG integration tests for arbitrary impact of sample order changes on downsampling	2011-10-04 08:14:00 -07:00
indels	RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.	2011-10-06 15:57:49 -04:00
phasing	Update to new RodBinding system	2011-08-11 17:54:16 -04:00
qc	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
recalibration	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
validation	Continuing progress towards RodBinding 1.0	2011-08-03 17:19:28 -04:00
varianteval	SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers.	2011-09-23 16:06:52 -04:00
variantrecalibration	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
variantutils	a) Cleanups/bug fixes to previous commit to CombineVariants.	2011-09-24 19:08:00 -04:00
BAQIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
PileupWalkerIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00