Merge pull request #49 from COMBINE-lab/develop

Fixed some bugs related to analyse_runs
Fix list returned by statistics.get_stratified_stats_types().

Had previously changed the caller of this functions to remove ** parameter
magic, but this means that the object returned needs to be a list of tuples,
not a list of maps.
GROUPED_THRESHOLD parameter missing for 'analyse_runs' command.

Which meant its default value was not available. Also need to fix fact that
although validation was being run plain _PiquantOptions, the option map was not
being updated with the validated values (i.e. the value for GROUPED_THRESHOLD
would remain as a string, not converted to an int).
More finely-grained params for piquant.py plotting functions.
Protect for case of option having no value.
More docs updates for v1.1.
Add script/commands description to usage messages.

Fixes #48.
Updates to RSEM quantifier for v1.2.19.

No polyA tails is now the default, and it must be explicitly specified to build
a bowtie index for the transcript reference.

Fixes #41. No code changes were needed for updating Cufflinks 2.2.0 -> 2.2.1.