Eric Banks 1e90d602a4 Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.		2011-12-14 13:38:20 -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	Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.	2011-12-14 13:38:20 -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	Queue now properly escapes all shell arguments in generated shell scripts	2011-12-01 18:13:44 -05:00
utils	Bug fix for complex records: do not ever reverse clip out a complete allele.	2011-12-14 11:21:28 -05:00