chartl 21ec44339d Somewhat major update. Changes: ... - ProduceBeagleInputWalker + Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present + Takes a bootstrap argument -- can use some given %age of the validation sites + Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap -BeagleOutputToVCFWalker + Now filters sites where the genotypes have been reverted to hom ref + Now calls in to the new VCUtils to calculate AC/AN -Queue + New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype + full calling pipeline v2 uses the above libraries + minor changes to some of my own scripts + no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-08 13:30:28 +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	Somewhat major update. Changes:	2010-10-08 13:30:28 +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/gatk/walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
utils	At some time in the recent past, we lost our ability to process the '-L all'	2010-09-30 15:58:43 +00:00
BaseTest.java	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +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