chapmanb/bcbio-nextgen — pull request #104 by lbeltrame (2013-09-12 14:25:59+00:00)
Title: Ensure only MuTect 1.1.5+ is used when doing tumor analysis

This pull request implements a version check that raises a `ValueError` in case MuTect's version is less than 1.1.5 (1.1.4 had Java incompatibilities), and removes the "error hacks".

Unfortunately, due to an issue (https://github.com/broadinstitute/mutect/issues/5) MuTect doesn't properly report its version, so a rather stupid hack is used instead.

Please review and comment on whether this is a good approach.