Eric Banks 54331b44e9 New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.		2011-11-02 12:47:30 -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	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
commandline	For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?	2011-10-27 23:54:28 -04:00
gatk	New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.	2011-11-02 12:47:30 -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	New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.	2011-11-02 12:47:30 -04:00