kshakir 2058fc12bc Small bug fixes: ... Added a property to allow generating Queue extensions around an external version of the GATK. Updated argument order in -help. Restored the ability to use QScript trait imported annotations in constructors. Removing line feeds from email password files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5416 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-10 19:54:14 +00:00
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engine	Small bug fixes:	2011-03-10 19:54:14 +00:00
extensions	Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error:	2011-03-07 04:29:06 +00:00
function	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
library	Fix for expanded intervals in the case where the input file has overlapping intervals in it (seriously?)	2011-02-28 19:56:33 +00:00
pipeline	Fixing up the output system of the Unified Genotyper. Deprecating the -all_bases and -genotype arguments. Adding instead the --output_mode (EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES) and --genotyping_mode (DISCOVERY, GENOTYPE_GIVEN_ALLELES) arguments. UG now does the correct thing when passed alleles (bound to the 'alleles' rod) to use for genotyping; added several integration tests to cover this case. This commit will break the batched calls merging script, but Chris knows this and is ready for it...	2011-02-22 06:07:18 +00:00
util	Small bug fixes:	2011-03-10 19:54:14 +00:00
QCommandLine.scala	GSA-423 Better reporting for errors in QScript.script().	2011-02-18 22:21:15 +00:00
QException.scala	Fix for Queue	2010-09-12 15:18:08 +00:00
QScript.scala	Small bug fixes:	2011-03-10 19:54:14 +00:00
QScriptManager.scala	Due to recent LSF hiccups put a very brief (.5-2min) retry around getting status. Can't wait too long because statuses are archived an hour after exit.	2011-02-23 18:59:08 +00:00
QSettings.scala	Small bug fixes:	2011-03-10 19:54:14 +00:00