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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AllLocusViewUnitTest.java	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
CoveredLocusViewUnitTest.java	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
LocusReferenceViewUnitTest.java	Merging the sharding-specific inherited classes down into the base.	2010-06-17 22:36:13 +00:00
LocusViewTemplate.java	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
ReadBasedReferenceOrderedViewUnitTest.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
ReadReferenceViewUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
ReferenceOrderedViewUnitTest.java	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
ReferenceViewTemplate.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
ShardDataProviderUnitTest.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