MANTA-27 allow spaces in input filenames
close misc os x compatability issues
update for clang 3.4
Added some simple code to clean the SA tag by removing the trailing semi-colon.
Update cppcheck script for v1.63
add new util script
MANTA-117 somatic likelihood scoring
MANTA-117 clarify debug statement
MANTA-117 refresh source formatting
MANTA-117 close misc compiler warnings
MANTA-117 original qscore design + minor refactor

restor original qscore design to see how far alternate
parameterization can get us
MANTA-117 some additional edits to start test
MANTA-117 add a somatic score vcf filter

Also expose all germline and somatic score cutoff in the manta config
file.
MANTA-117 activate new qscore threshold options
MANTA-117 add noise state to the somatic score
MANTA-117 add two tier somatic score
MANTA-117 initial parameter adjustment
add somaticscore filter
fix up debug output
MANTA-117 rebalance somaticscore parameters