updating runStrelka.sh for snps as well as indels
Added option --list_tools to RunBenchmark.
--This prints out the list of available scripts and exits
--Added a LIB_DIR base directory to all of the relative file paths
Fixing documentation typo.
Adding check for required files at the start of GenerateBenchmark.scala
--Things should fail immedietly now instead of running for a while.
Fixing null pointer when there is a missing root directory.