ebanks ab9ffb1a74 Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5711 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-29 16:03:45 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	A fix for Marian Thieme's NPE in the new sharding system.	2011-04-21 19:47:14 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
report	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
traversals	Fix requested by Lee Lichtenstein: first check to see whether it's time for	2011-04-20 03:22:48 +00:00
walkers	Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case.	2011-04-29 16:03:45 +00:00
CommandLineExecutableUnitTest.java	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +00:00
GenomeAnalysisEngineUnitTest.java	Fix for bug GSA-449: Intervals that are not in GATK format are not validated	2011-04-27 18:12:10 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00