Adding modified scripts.
Adding a python wrapper to run fracturebams and mergebams
many changes, some things seem to be running now
fixed problems that were preventing make_fn_sim_datasets.pl from running
Putting the right create_1g_sim_data.pl in.  Adding a bam_info file as an example.
Changed indel file to be the gatk gold standard.
Changed make_vfs to take the indel file as a parameter.
Changed runAllCombinations to not use files from Kris' directories.
Merge branch 'master' of /home/unix/louisb/xchip/indelocator-benchmark/new-bams/../sim-updated
Adding a Queue script to run the whole benchmark process.  It is currently wildly incomplete.
Figured out the issues with GenerateBenchmark.scala that was making it completely fail.  I needed to either delete the hidding .done files or invoke Queue with the -startFromScratch option.
Working on generate benchmark.  It is currently in a totally broken transition state.
Adding .gitignore.
Working on GenerateBenchmark.scala.
The current state doesn't compile.
Getting GenerateBenchmark to compile, dealing with the incorrect type signatures that I hadn't understood.
Changing from invoking SomaticSpike as a walker to it being a generic commandline invocation.  Still not running.
Fixed the problem I was having.  It was related to the file loading rather than the SomaticSpike bindings.
Added make_fn_sim functionality to GenerateBenchmark.
Fixed the missing directory issue with fracture bam.
Merge branch 'master' of /home/unix/louisb/xchip/indelocator-benchmark/new-bams/../sim-updated