WIP on haplotype calling
cleaned up memory and thread requests a little for GATK plugin
updates to gatk code
now handles situation where manyTasklet does not actually launch any jobs. Wait for many simply finishes if no children to wait on
Merge branch 'develop' into variantCalling
further fix of exit status processing for listenForManyTasklet
Merge branch 'develop' into variantCalling
* only add some debug msg to the jobSubmissionController
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
updated so can now remove a file / filegroup from the file server and
mark as deleted and inactive in the database
Merge branch 'develop' into variantCalling

Conflicts:
	wasp-core/src/main/java/edu/yu/einstein/wasp/service/FileService.java
* Fixed the cell selection bug
* Improve bug fixed for cell selection
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/aj into develop
Merge branch 'develop' into variantCalling
updated gatk pipeline up to combined genotyping
Added SnpEff and VcfTools plugins
some minor cleanups
Fixed problem with job viewer miscounting total jobExecutions to show
when subsets selected