Created improved variant frequency calculation class and basic reviewdir reading classes
More progress on computing and annotating new ARUP frequency data
Updated ComputeVarFreq and ARUPDB annotations to produce results based
on percentage of samples tested instead of raw totals.
Fixed issue in MultiOperator where reference files were added to list of
normal input files, which caused some operators to crash.
Created new class to find jar file creation time and path so we can
always tell which version of Pipeline was being used from the log file
and qc info.
Minor updates to QCJsonReader, fixed -S issue in MultiRemoveDups
Added code to allow parameters to be specified in the template.
Merge branch 'master' of https://mebbert@bitbucket.org/arup-ngs/pipeline.git
Resolved conflict in MultiRemoveDups where both Mark and Brendan fixed the same problem
Added GenerateVCF class to create simulated vcfs which can then be applied to a reference prior to read simulation
Added trimming operator for haloplex fastqs