hanna 3dc78855fd Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax ... (-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-25 03:47:57 +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	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
ReferenceViewTemplate.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
ShardDataProviderUnitTest.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