hanna 09c7ea879d Merging GenomeAnalysisEngine and AbstractGenomeAnalysisEngine back together. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4889 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-21 02:09:46 +00:00
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storage	Merging GenomeAnalysisEngine and AbstractGenomeAnalysisEngine back together.	2010-12-21 02:09:46 +00:00
stubs	Fixed recently introduced multiplexer issue where DoC couldn't be written	2010-12-14 19:35:15 +00:00
DirectOutputTracker.java	Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem.	2009-09-15 21:06:45 +00:00
OutputTracker.java	Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.	2010-09-25 02:49:30 +00:00
StingSAMFileWriter.java	setMaxRecordsInRam now a member of StingSAMFileWriter.	2010-08-27 14:50:41 +00:00
ThreadLocalOutputTracker.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