Ensure only MuTect 1.1.5+ is used when doing tumor analysis #104
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it reports the GATK version it is based on instead: until this is fixed, we use a hack knowing that 1.1.4 is based on GATK 2.2 and 1.1.5 on GATK 2.7.
| if self._mutect_version is None: | ||
| self._set_default_versions(self._config) | ||
| if self._mutect_version is not None: | ||
| return self._mutect_version |
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You could skip the explicit version checking of the jar and just use the value generated in _set_default_versions(). This is derived from the jar name, which is just another hack but at least we're only hacking the version in one way. Then I'd just return assert that _mutect_version is not None and return that value. We can add an explicit version check if they add it in the future.
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Luca; |
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As you requested, I removed the running and relied only on the cached version. Let me know if this is what you meant. |
Ensure only MuTect 1.1.5+ is used when doing tumor analysis
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Luca -- looks great. Thanks again for adding this in. |
This pull request implements a version check that raises a
ValueErrorin 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 (broadinstitute/mutect#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.