Merge pull request #1 from cancerit/master

Basic code import from test scripts
First cleaned up version
Working codebase for comtamination, matched-ness and gender checks
Minor change to check for alleleCounter and update distribution name appropriately.
corrected problem checking for dependancy
Enable ability to send json to a file instead of just STDOUT
copy paste correction
forgot to update dist name in modules
add additional warnings to aid debugging
forgot to change parameter capture
Corrects issue with getting path of verifyBamId and bump version to 1.0.0
Merge pull request #2 from cancerit/develop

Roll 1.0.0