ebanks 4e83ba411f 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 00:18:17 +00:00
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arguments	Removing the obsolete --hapmap and --hapmap_chip options	2010-08-31 16:57:05 +00:00
contexts/variantcontext	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
datasources	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
executive	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
filters	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
iterators	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
refdata	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
traversals	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
walkers	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