Mauricio Carneiro 389380a590 ReduceReads ref bases are now output as '=' to save space ... Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.		2011-10-30 12:04:39 -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	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -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	ReduceReads ref bases are now output as '=' to save space	2011-10-30 12:04:39 -04:00