delangel 5af986e0c1 Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3897 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-29 18:49:22 +00:00
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HLAcaller	Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.	2010-07-19 19:10:29 +00:00
annotator	1) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +00:00
duplicates	forgot to update md5s	2009-12-29 20:31:29 +00:00
poolseq	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
validation	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
vcftools	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
BeagleIntegrationTest.java	Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker)	2010-07-29 18:49:22 +00:00
ClipReadsWalkersIntegrationTest.java	-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically	2010-03-17 16:00:10 +00:00
HapmapPoolAllelicInfoIntegrationTest.java	Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg.	2009-12-14 22:42:50 +00:00