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
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TraverseDuplicatesUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
TraverseReadsUnitTest.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