Favor direct sequential output

[a-ludi]

Since the loop shall be removed from the main algorithm, the result can be sequentially written to stdout at the end. Thus, OverlayDB only adds unnecessary complexity and shall be removed.

Tasks

• In the "finish" step of the algorithm…
  • determine a linear walk contigs taking the gap filling information and scaffolding information into account
  • collect all extensions, gap insertions and cropped contigs
  • write them to stdout
• Remove CoordinateTransform
• Remove OverlayDB