hanna acfe83920b '-L unmapped': adding integration tests for explicitly including (-L unmapped) ... unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting the suite of unit tests already put in place. '-L unmapped' seems safe to use; go for it, but please validate results against samtools flagstat when the process finishes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-15 23:11:46 +00:00
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IntervalFileMergingIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
IntervalIntegrationTest.java	'-L unmapped': adding integration tests for explicitly including (-L unmapped)	2010-12-15 23:11:46 +00:00
IntervalUtilsUnitTest.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
NwayIntervalMergingIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00