Handle absence of MD tags better about pebbles

[nickzoic]

Yep, so plugins now get passed a "logger" object, which can be used to report non-fatal errors, warnings, info messages and also progress. In the GUI, these will get displayed under the 'preview' pane. In the command-line application these get logged to stdout and stderr.

[nickzoic]

In #6 I kinda had to reproduce the logic from call_mutations_from_pysam so I could catch and log this, but it's not really a good way to do it.

[genomematt]

Now fixed in dev0.3 branch passing countess logger into relevant pebbles functions