ebanks dd23f204ab Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4283 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 01:54:50 +00:00
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alignment	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
analyzecovariates	All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException.	2010-09-10 15:25:30 +00:00
commandline	Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException	2010-09-14 22:45:15 +00:00
gatk	Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki.	2010-09-15 01:54:50 +00:00
oneoffprojects	We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later.	2010-09-15 00:18:17 +00:00
playground	ReadBackedPhasing silently ignores sites with ploidy != 2	2010-09-13 21:14:17 +00:00
queue	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
utils	Added a back door so that integration tests can reset the sequence dictionary	2010-09-14 18:58:08 +00:00