2.0.0 - DVF filter and improved UI

Introducing the DVF flag, to flag variants which arise from duplicated reads with PCR stutter. In addition to being independently useful, the DVF flag tackles a relatively rare issue users have experienced where internal dupmarking of supporting reads for a given variant left insufficient remaining reads to test ADF and ALF, allowing spurious variants to escape unflagged. These variants would now be flagged DVF. Note that this is not the only use of the DVF flag, as variants may be flagged DVF regardless of the result of their tests for other flags. See the README for info on relevant parameters.

This release also introduces some breaking UI changes - namely that the tool now outputs to stdout, and may be redirected to file using standard shell operations (e.g. ">"); that the name mapping flag now takes a JSON file or JSON-formatted string; and that alignment format is now auto-detected so the format flag is no longer needed. See the README for more details on these, and other more minor UI changes.

Full Changelog: 1.2.0...2.0.0