2.0

Breaking changes

• Folder outputs have different and sequential names
• Some modules have their own folders now (like trimming)
• map_summary.sh now summarizes a single map

New Features

• config.yaml has a new parameter
• new optional scripts for:
  • map refinement
  • iterating JoinSingles2All
  • setting a hard LG maximum and reassigning all those exceeding it to group 0

Fixes

• The original map_summary.sh didn't always accurately summarize the data and has been replaced with map_summary.r