aaron 50f32b7f61 Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@718 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-14 21:20:18 +00:00
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gatk	Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way.	2009-05-14 21:20:18 +00:00
utils	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
BaseTest.java	Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.	2009-05-14 21:06:28 +00:00
TrivialInstrumenter.java	Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.	2009-05-14 16:52:18 +00:00