Improved Reporting RC1

The main change in this release was to add several lines to the coverage reports: #313 (rejected data), #345 (deletions), #337 (soft clipping), and #338 (insertions).

Other changes:

• #344 replace R coverage maps with Python version
• #343 several improvements to how the monitor handles cancelled runs and purged results
• #340 consensus for two references drifted past each other

For the full list, see the milestone.