depristo c7445a6fbd Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5543 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-31 16:49:39 +00:00
..
alignment	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
analyzecovariates	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
commandline	Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.	2011-03-29 21:04:09 +00:00
datasources/pipeline	FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.	2011-02-17 19:09:03 +00:00
gatk	Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us.	2011-03-31 16:49:39 +00:00
jna	Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.	2011-03-10 22:58:54 +00:00
oneoffprojects	Minor changes to MannWhitneyU:	2011-03-30 17:03:02 +00:00
playground	Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.	2011-03-29 21:04:09 +00:00
queue	Minor updates to match the wiki documentation.	2011-03-24 20:22:23 +00:00
utils	Minor changes to MannWhitneyU:	2011-03-30 17:03:02 +00:00