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gatk-3.8/java/test/org/broadinstitute/sting
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kshakir 4ed9f437e9 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 
The GAE half has all the walker specific code.  The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-23 23:28:55 +00:00
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alignment all fixed..thanks Matt! 2010-09-10 06:18:59 +00:00
commandline Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
datasources/pipeline Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
gatk Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 2010-09-23 23:28:55 +00:00
oneoffprojects/walkers The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 2010-09-21 18:21:22 +00:00
playground removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. 2010-09-15 22:54:49 +00:00
utils removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. 2010-09-15 22:54:49 +00:00
BaseTest.java Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
WalkerTest.java Added a back door so that integration tests can reset the sequence dictionary 2010-09-14 18:58:08 +00:00