Laurent Francioli 16cc2b864e - Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT ... Signed-off-by: Ryan Poplin <rpoplin@broadinstitute.org>		2011-12-19 10:30:59 -05:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	- Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT	2011-12-19 10:30:59 -05:00
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	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
diffengine	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
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	Forgot to update the unit test	2011-12-18 01:13:49 -05:00
indels	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
phasing	Merge with master	2011-11-19 09:56:06 -05:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Update MD5s for SOLiD recalibration	2011-10-13 18:01:51 -04:00
validation	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
varianteval	Updated md5sum for MendelianViolationEvaluator test to reflect the change in column alignment in VariantEval.	2011-12-12 12:22:43 +01:00
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	Bug fix: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case.	2011-12-19 10:04:33 -05:00
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
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	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00