Merge pull request #10 from chapmanb/master

Merge from Brad upstream
Merge pull request #11 from chapmanb/master

Support for TopHat 2.0.9: handle extra paired end output with single-mat...
Merge pull request #12 from chapmanb/master

Merge final version 0.7.3 from Brad upstream
Better info for when jar_versioner can't determine version
Issue warning but do not exit when muTect version is empty
Merge pull request #120 from mariogiov/mutect_version_check

Mutect version check
Merge pull request #121 from mariogiov/jar_versioner_info

Jar versioner info