depristo 1bd1404aa9 Sometimes md5s can be null ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5867 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-24 19:17:18 +00:00
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alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	WalkerTest now checks for valid md5s in the integrationtests themselves, so no more stray whitespace errors. Added a WalkerTestTest to ensure tha t bad MD5s are detected and an error thrown	2011-05-24 14:34:55 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.	2011-05-23 18:06:05 +00:00
playground/gatk/walkers	PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only.	2011-05-11 12:07:44 +00:00
utils	Make IntervalIntegrationTest aware of the new alignments in the MV1994.bam	2011-05-23 19:59:47 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Sometimes md5s can be null	2011-05-24 19:17:18 +00:00