Joel Thibault 97d29f203e Add walltime changes to LSF ... - Check whether the specified attribute is available - Add pipeline test (disabled due to missing attribute)		2012-11-29 15:23:37 -05:00
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engine	Add walltime changes to LSF	2012-11-29 15:23:37 -05:00
extensions	Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars.	2012-10-23 14:08:31 -04:00
function	Add walltime changes to LSF	2012-11-29 15:23:37 -05:00
library	Fix edge case for very small VCFs	2012-01-19 00:51:28 -05:00
util	Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)	2012-11-21 15:56:53 -05:00
QCommandLine.scala	Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.	2012-11-14 10:33:20 -05:00
QCommandPlugin.scala	Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.	2012-11-14 10:33:20 -05:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.	2012-11-14 10:33:20 -05:00
QScriptManager.scala	Fixed package error and a few deprecated scala warnings.	2012-10-15 15:29:40 -04:00
QSettings.scala	Add walltime changes to LSF	2012-11-29 15:23:37 -05:00