carneiro 8ea71fd294 minor dataset chages. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5289 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-22 20:18:10 +00:00
..
qscript	minor dataset chages.	2011-02-22 20:18:10 +00:00
src/org/broadinstitute/sting	Fixing up the output system of the Unified Genotyper. Deprecating the -all_bases and -genotype arguments. Adding instead the --output_mode (EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES) and --genotyping_mode (DISCOVERY, GENOTYPE_GIVEN_ALLELES) arguments. UG now does the correct thing when passed alleles (bound to the 'alleles' rod) to use for genotyping; added several integration tests to cover this case. This commit will break the batched calls merging script, but Chris knows this and is ready for it...	2011-02-22 06:07:18 +00:00
test/org/broadinstitute/sting/queue	Defaulting the MFCP to run without a tear script.	2011-02-17 21:13:14 +00:00