hanna 0c99c97685 The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified. ... Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line arg headers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-22 15:27:58 +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
gatk	The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.	2010-09-22 15:27:58 +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