Update GMT::Bsmap::MethRatio

Supersedes #244.

Before merging I would like to update the tests so they actually run `methratio.py`.
My hope was that passing the inputs to `Genome::Sys->shellcmd` would be sufficient file checking:

```
my $return = Genome::Sys->shellcmd(
    ...
    input_files => [$self->bam_file, $self->_reference_fasta],
);
```

But I am willing to add explicit validations if you think that's better!