chartl 0c54aba92a Changes: ... @VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object. @AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones. @ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true. Added: @PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-11 15:01:50 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Changes:	2009-09-11 15:01:50 +00:00
test/org/broadinstitute/sting	So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday).	2009-09-10 14:28:43 +00:00