hanna c806ffba5f Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations ... will not be as fast as they could be because the workflow is currently merge sam records (sharding) -> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext is updated to take advantage of the new functionality in ReadBackedPileup. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 02:11:42 +00:00
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annotator	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +00:00
concordance	adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI.	2010-06-18 08:23:23 +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	Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.	2010-04-29 22:50:17 +00:00
filters	adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI.	2010-06-18 08:23:23 +00:00
genotyper	Refactoring of the annotation system:	2010-06-09 17:05:51 +00:00
indels	When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads.	2010-06-16 19:36:36 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	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
sequenom	Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.	2010-04-19 05:47:17 +00:00
varianteval	Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.	2010-06-18 21:51:40 +00:00
variantrecalibration	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +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	adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI.	2010-06-18 08:23:23 +00:00