ebanks f742980864 1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon. ... 2. Moved Jared's VCFTool code into archive so that everything would compile. 3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader. 4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-20 06:16:45 +00:00
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annotator	The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly.	2010-07-14 04:56:58 +00:00
concordance	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-13 00:56:12 +00:00
coverage	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +00:00
fasta	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
filters	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
genotyper	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +00:00
indels	Re-enable (most of) these tests. Guillermo will re-enable the other one when the VCF->VC conversion is done for indels	2010-07-18 03:24:28 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too.	2010-07-19 22:13:18 +00:00
sequenom	Refactoring the VCF writer code; now no longer uses VCFRecord or any of its related classes, instead writing directly to the writer. Integration tests pass, but some are actually broken and will be fixed this week.	2010-07-18 13:19:56 +00:00
varianteval	Parallelized CountCovarites! percent_ref_called_var now a standard genotype concordance module (for validation!). Really much smarter merging of headers for combineVariants. VCF codecs now actually look at the file version and blow up if they are the wrong versions. setHeaderVersion() in VCFHeaderLine.	2010-07-16 14:10:18 +00:00
variantrecalibration	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00
variantutils	CombineVariants tests for Guillermo and Eric to explore the correctness of the in/out reader, writer behavior of the system.	2010-07-19 22:41:48 +00:00
PileupWalkerIntegrationTest.java	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +00:00
PrintReadsWalkerUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
VariantsToVCFIntegrationTest.java	First step in major cleanup/redo of VCF functionality. Specifically, now:	2010-07-16 22:49:16 +00:00