cleaned up whitespace and removed testing code
tool to plot coverage over target regions. And hey, I even wrote a crappy test
Merge branch 'capturePlot'
fixed test
Updated `genome` tab completion.
Updated `gmt` tab completion.
MC16s: add clusters to solexa inst data for est kb usage
Better error checking for Bwasw
If we subtract one from the VCF coord then we need to add it back when
we output it. Also, we should check that our filehandles opened.

CHANGELOG: Fix VCF output for liftover tool (had an off by one error).
Old data is gone again, so update blessed build blindly.
Bring back defaults required for MGAP pipeline...
ensure changes to inputs or other model properties are applied to new models, not just processing profile changes
make processing-profile diff flag differing properties