Correct 2 'my'  declarations masking earlier declarations of @keys and @vals.
Increase width and height of graph layout for higher resolution screen.
Changed names of bed files
Merge remote-tracking branch 'js10-remote/bed' into devel

Conflicts:
	data/tophat2_sample_template.vtf
Minimal test data files
try to capture all child exits by waiting before killing process group
Check use of STDIN and STDOUT if EXEC node use_STD{IN,OUT} keys provided
Cope with Boolean in JSON
use_STD{IN,OUT} in produciton RNAseq pipeline
use bammarkduplicates2 in place of bammarkduplicates in prod RNAseq Tophat2 pipeline
remove commented and non-functional code
Merge pull request #14 from dkj/devel

Improve exiting child reporting, add EXEC std{in,out} validaiton, and use bammarkduplicates2 in RNAseq analysis
give alignment filter output default json suffix reflecting its content
Name change for WTSI DNA Pipelines second stage RNAseq pipeline
Initial adaptation of WTSI production RNA-Seq pipeline without PhiX separation
Provide Tophat parameter for stranded nature of RNA
Change description of the pipeline and file name
Merge remote-tracking branch 'wtsi-npg/devel' into devel
Merge pull request #15 from Ichbalanke/devel

Non-PhiX RNA-Seq pipeline
Merge remote-tracking branch 'wtsi-npg/devel' into devel