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gatk-3.8/java/test/org/broadinstitute/sting/gatk/datasources/providers
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depristo cd8321cdc9 Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5525 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-27 20:48:24 +00:00
..
AllLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
CoveredLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
LocusReferenceViewUnitTest.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
LocusViewTemplate.java Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call. 2011-03-27 20:48:24 +00:00
ReadBasedReferenceOrderedViewUnitTest.java Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
ReadReferenceViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReferenceOrderedViewUnitTest.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
ReferenceViewTemplate.java Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns. 2010-12-05 18:29:39 +00:00
ShardDataProviderUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00