Eric Banks 827fe6130c Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one).		2011-09-01 11:40:35 -04:00
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alignment	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
analyzecovariates	AnalyzeCovariates uses the general RScript system now	2011-08-27 12:54:13 -04:00
commandline	Better error message when you cannot determine a ROD type because the file doesn't exist or cannot be read	2011-08-23 10:56:37 -04:00
gatk	Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one).	2011-09-01 11:40:35 -04:00
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
queue	Fixed Queue's tagging of RodBindings.	2011-08-21 02:34:20 -04:00
utils	Merge branch 'master' into rr	2011-08-30 02:50:19 -04:00