Khalid Shakir 7486696c07 When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. ... Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory. Updated various tests for above items and other small fixes.		2011-12-16 18:09:25 -05:00
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engine	Swapping Thread.sleep(0) with Object.wait(0) caused Queue to lock up. Thanks to rpoplin for pointing it out.	2011-10-28 15:51:03 -04:00
extensions	Queue now properly escapes all shell arguments in generated shell scripts	2011-12-01 18:13:44 -05:00
function	Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction	2011-12-05 14:06:00 -05:00
library	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.	2011-11-17 13:56:42 -05:00
util	Support for NT testing (default up to 4) for CC and UG	2011-12-14 18:45:00 -05:00
QCommandLine.scala	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	Now captures the exechost in the job report	2011-08-28 12:05:56 -04:00
QScriptManager.scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
QSettings.scala	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00