Mauricio Carneiro 07128a2ad2 ReadUtils cleanup ... * Removed all clipping functionality from ReadUtils (it should all be done using the ReadClipper now) * Cleaned up functionality that wasn't being used or had been superseded by other code (in an effort to reduce multiple unsupported implementations) * Made all meaningful functions public and added better comments/explanation to the headers		2011-12-20 17:48:40 -05:00
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alignment	GATKSAMRecord refactor	2011-11-03 15:43:26 -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	A toString() method for IntervalBindings	2011-11-23 11:56:12 -05:00
gatk	ReadUtils cleanup	2011-12-20 17:48:40 -05:00
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
queue	General improvements to Queue	2011-12-20 14:05:09 -05:00
utils	ReadUtils cleanup	2011-12-20 17:48:40 -05:00