droazen d323ef0461 As promised, VariantFiltration can now mask out sites within a user-specified window around the provided mask rod. By default the window is 0, but you can now use the --maskExtension argument to increase that value. Added integration tests to cover this new functionality. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6060 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-22 22:55:29 +00:00
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annotator	Annotations used to build the 1000G consensus callsets are now standard annotations	2011-06-09 17:03:39 +00:00
beagle	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
coverage	-ct x no longer includes coverage in the previous bin	2011-02-24 15:52:04 +00:00
fasta	Fixing broken walker as per GS; adding integration test to cover it.	2011-06-22 22:54:04 +00:00
filters	As promised, VariantFiltration can now mask out sites within a user-specified window around the provided mask rod. By default the window is 0, but you can now use the --maskExtension argument to increase that value. Added integration tests to cover this new functionality.	2011-06-22 22:55:29 +00:00
genotyper	Annotations used to build the 1000G consensus callsets are now standard annotations	2011-06-09 17:03:39 +00:00
indels	Changing the default behavior of the IndelRealigner to run without Smith-Waterman. Changed around the integration tests accordingly.	2011-06-22 22:53:58 +00:00
phasing	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
qc	Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings.	2011-05-23 21:32:53 +00:00
recalibration	Surprisingly, the TileCovariate was indeed covered in integration tests. Updated.	2011-06-14 17:40:23 +00:00
sequenom	continuing from last night, the integration tests weren't covering the right behavior either	2011-04-28 13:30:57 +00:00
varianteval	Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF	2011-06-19 03:11:00 +00:00
variantrecalibration	Misc cleanup in VQSR.	2011-06-09 18:37:37 +00:00
variantutils	Slightly more extensive test includes a 0/0 site to genotype	2011-06-08 14:48:55 +00:00
BAQIntegrationTest.java	Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.	2011-01-28 15:08:21 +00:00
ClipReadsWalkersIntegrationTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PileupWalkerIntegrationTest.java	Updated to now longer include 2nd-best base output	2011-04-03 20:13:10 +00:00
PrintReadsIntegrationTest.java	Added integration test for -n parameter	2011-06-22 22:53:22 +00:00
PrintReadsWalkerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00