Adding RunCallersOnKDB.scala
This is a QScript which runs a mutation caller on the Knowledge base datasets and calculates performance metrics.
It is currently far from complete.
Added evaluation and aggregation steps.
Adding new quick running mutect script
Adding mutect oncotation pipeline stages.
Moved functions_mara.R and kdb_annotate.R into this folder.
This should be reverted later, but it's easiest for now.
Added untested ability to load pairs from a file.
Added a testpairs.txt file which should be loaded automatically.
Adding a summary output step
Added a warpper for countFPs
Adding countFP.R
Moving and refactoring the collection step so that it doesn't have timing issues with queue.
Trying to solve file depencies in qscript.
messing around trying to understand what's happening
More messing about trying to link the tasks appropriately.  It seems like lists might be prefered to seqs?
Fixing memory limit and adding NN counting
Removing 'WEX' parameter from annotate kdb because it doesn't do what i think it does.
Fixing Evaluator issue.
Updating testpairs.txt to have more pairs and test actually aggregating things.
Fixed bug caused by a missing val statment that was breaking the q-graph for CountFP.
Added identifierString to the aggregated output file name.
Including the report generator.
Changing sensitivity/specificity to recall/precision/f1.