hanna
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8d2c14b29c
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Update Picard / sam-jdk at Tim's request.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-03 02:17:25 +00:00 |
depristo
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a3729bd59c
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Now I call BeforeMethod correctly
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4872 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-17 22:45:45 +00:00 |
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depristo
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b7e4a015c0
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static thread cache reset in UnitTest
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4870 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-17 21:53:10 +00:00 |
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depristo
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3bbc6a0540
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Slightly more thread safe CachingIndexedFastaSequenceFile.java. Likely passes parallel testing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4869 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-17 21:05:17 +00:00 |
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depristo
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4a54f3f230
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ThreadLocal version of CachingIndexedFastaSequenceFile. More efficient support for shared memory BAQ calculations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4865 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-17 15:44:48 +00:00 |
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depristo
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44feb4a362
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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
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2010-12-05 18:29:39 +00:00 |