ebanks ca4eab1d23 Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields. ... Added an integration test for the read-less case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-09 20:36:46 +00:00
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annotator	Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields.	2010-06-09 20:36:46 +00:00
concordance	Fixing/cleaning up the vcf merge util	2010-03-19 15:13:32 +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 This mean 'Variants' is no longer valid for a ROD type, use GeliText instead.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	Moving VariantFiltration over to use VariantContext.	2010-03-19 18:35:23 +00:00
genotyper	Refactoring of the annotation system:	2010-06-09 17:05:51 +00:00
indels	Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time.	2010-05-28 14:10:48 +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	updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version	2010-06-09 01:47:04 +00:00
variantrecalibration	Removing the Variant Recalibration Performance test because it isn't ready yet.	2010-05-28 18:27:25 +00:00
PileupWalkerIntegrationTest.java	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +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 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