12 Commits (7506994d09c4dfb4a66fb23b76f8d8a1aba0714b)

Author	SHA1	Message	Date
Mark DePristo	7506994d09	Nearing final BCF commit ... -- Cleanup some (but not all) VCF3 files. Turns out there are lots so... -- Refactored gneotype parser from VCFCodec and VCF3Codec into a single shared version in AbstractVCFCodec. Now VCF3 properly handles the new GenotypeBuilder interface -- Misc. bugfixes in GenotypeBuilder	2012-06-14 16:42:32 -04:00
Khalid Shakir	89a581a66f	Added ability to specify arguments in files via -args/--arg_file ... Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()	2011-10-24 15:58:34 -04:00
Mark DePristo	3af001fff2	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
Mark DePristo	c2287c93d7	Cleanup of codec locations. No more dbSNPHelper ... -- refdata/features now in utils/codecs with the other codecs -- Deleted dbsnpHelper. rsID function now in VCFutils. Remaining code either deleted or put into VariantContextAdaptors -- Many associated import updates due to code move	2011-08-18 10:02:46 -04:00
Mark DePristo	40e06f9afb	Fixed broken RodBinding defaults. ... -- Verified now to be correct at runtime -- UnitTest covers this -- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.	2011-08-11 08:58:30 -04:00
Mark DePristo	0810c42309	GATK now does dynamic type determination for VCF files ... Added UnitTests covering all of the cases.	2011-08-08 14:45:46 -04:00
Mark DePristo	573700d18d	Adding missing import	2011-08-04 21:57:00 -04:00
Mark DePristo	14e43c3382	Final fix to RodBindingUnitTest to reset global counter variable	2011-08-04 21:52:39 -04:00
Mark DePristo	d0279bb28c	RodBinding names are now defaulting to the ArgumentTypeDescriptor fullname ... Nearly all of the tools are passing integrationtests	2011-08-03 20:48:11 -04:00
Mark DePristo	2874835997	Bug fix for type checking RodBindings ... Now compares the feature class not the codec class. UnitTests improvements integrationtests on their way to actually running	2011-08-02 22:25:41 -04:00
Mark DePristo	b5e843f8f0	Approaching the end for the new RodBinding system ... -- support for explicit naming of bindings (-X:name,type x) -- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2) -- ParserEngineUnitTest expanded to cover all of the Rodbinding cases -- RodBindingUnitTest tests all of the low-level accessors -- Parsing engine throws UserExceptions when bad bindings are provided on the command line	2011-08-02 22:00:06 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00