fromer 947cc44854 Thanks to Matt for walking me through a proper version of VCF_BAM_utilities! Feel free to add to it, or use it to get the samples in a VCF file, a BAM file, or a collection of BAM files ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5223 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-09 18:08:27 +00:00
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engine	After code review with APSG, trying a patch for SIGSEGV errors which checks the LSF result codes from lsb_openjobinfo instead of checking for a null return value from lsb_readjobinfo.	2011-02-08 21:08:22 +00:00
extensions	Checking if the interval files exist before using them to calculate the minimum scatter parts.	2011-01-31 18:07:34 +00:00
function	Copying jobLimitSeconds to clones.	2011-01-30 06:35:53 +00:00
library	Bug fixes in the in process function (spoiled by python: was not closing my writers). SortByRef now works somewhat like the perl script does, rather than doing a memory-expensive sort. Adding a QTools qscript which is kinda clunky, and will be used mostly for integration tests of these IPFs, pending some better way to construct argument collections and function accessors at compile-time.	2011-02-03 17:32:46 +00:00
pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
util	Thanks to Matt for walking me through a proper version of VCF_BAM_utilities! Feel free to add to it, or use it to get the samples in a VCF file, a BAM file, or a collection of BAM files	2011-02-09 18:08:27 +00:00
QCommandLine.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
QException.scala	Fix for Queue	2010-09-12 15:18:08 +00:00
QScript.scala	java changes:	2010-12-12 05:10:45 +00:00
QScriptManager.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
QSettings.scala	Cleaning up obsolete code.	2011-01-21 16:27:35 +00:00