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gatk-3.8/java/test/org/broadinstitute/sting/gatk/datasources/providers
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depristo 44feb4a362 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4792 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-05 18:29:39 +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 Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
LocusViewTemplate.java Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes. 2010-11-19 19:59:05 +00:00
ReadBasedReferenceOrderedViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReadReferenceViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReferenceOrderedViewUnitTest.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
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