ebanks c9c6ff49c2 Deprecated 'O' in favor of 'o' in the cleaner ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4085 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-23 18:09:24 +00:00
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annotator	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +00:00
coverage	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
fasta	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
filters	Adding command-line header to VA and VF	2010-08-08 05:21:15 +00:00
genotyper	Forgot to update UG performance test to reflect the new -o argument.	2010-08-23 00:57:16 +00:00
indels	Deprecated 'O' in favor of 'o' in the cleaner	2010-08-23 18:09:24 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
sequenom	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
varianteval	fixes for VariantEval integration tests affected by the spaces to underscores change.	2010-08-19 22:43:20 +00:00
variantrecalibration	Memory optimization for the VariantRecalibrator. Only add variants to the list if they pass the novelty and qual filters.	2010-08-17 21:57:28 +00:00
variantutils	Simple change to allow a list of samples or regular expressions to be provided in a text file (one line per sample).	2010-08-21 00:01:48 +00:00
PileupWalkerIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
PrintReadsWalkerUnitTest.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
VariantsToVCFIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00