Eric Banks 29662be3d7 Fixed bug where k=2N case wasn't properly being computed. Added optimization for BB genotype case not in old model. At this point, integration tests pass except for 1 case where QUALs differ by 0.01 (this is okay because I occasionally need to compute extra cells in the matrix which affects the approximations) and 2 cases where multi-allelic indels are being genotyped (some work still needs to be done to support them).		2011-12-03 23:12:04 -05:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	Adding Transmission Disequilibrium Test annotation to VariantAnnotator and integration test to test it.	2011-11-29 09:29:18 -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	DiffObjects no longer prints out the file name in the status so MD5 are stable	2011-10-10 15:10:57 -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	Fixed bug where k=2N case wasn't properly being computed. Added optimization for BB genotype case not in old model. At this point, integration tests pass except for 1 case where QUALs differ by 0.01 (this is okay because I occasionally need to compute extra cells in the matrix which affects the approximations) and 2 cases where multi-allelic indels are being genotyped (some work still needs to be done to support them).	2011-12-03 23:12:04 -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	VariantEval updates	2011-11-23 13:02:07 -05:00
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	Fix for changed MD5 in streaming VCF test	2011-11-23 19:01:33 -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