Guillermo del Angel f4b409fa0d CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result		2011-10-21 14:07:20 -04:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.	2011-10-12 15:44:54 -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	DiffObjects no longer prints out the file name in the status so MD5 are stable	2011-10-10 15:10:57 -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	Merged bug fix from Stable into Unstable	2011-10-11 12:03:51 -04:00
indels	Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.	2011-10-06 22:38:44 -04:00
phasing	Update to new RodBinding system	2011-08-11 17:54:16 -04:00
qc	Removing a public -> private dependency from the test suite.	2011-10-13 21:32:52 -04:00
recalibration	Update MD5s for SOLiD recalibration	2011-10-13 18:01:51 -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	CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result	2011-10-21 14:07:20 -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