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gatk-3.8/java/src/org/broadinstitute/sting/gatk/executive
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depristo 7880863eb7 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-12 15:07:38 +00:00
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Accumulator.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
HierarchicalMicroScheduler.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
HierarchicalMicroSchedulerMBean.java Basic instrumentation support for the hierarchical microscheduler.x 2009-05-29 22:19:27 +00:00
LinearMicroScheduler.java Massive cleanup of read filtering. 2010-08-11 20:17:11 +00:00
MicroScheduler.java Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. 2010-09-12 14:02:43 +00:00
OutputMergeTask.java General-purpose management of output streams. 2009-08-23 00:56:02 +00:00
ReduceTree.java Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing. 2009-04-29 20:26:16 +00:00
ShardTraverser.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
TreeReducer.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
WindowMaker.java Eliminated -mrl option. 2010-08-26 21:38:03 +00:00
package-info.java Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00