GBWTGraph v0.6

Some work on using GBWTGraph for GFA storage.

• Uses the vgteam fork of SDSL.
  • In CMake builds, uses the same SDSL as GBWT.
• When a GFA file contains both P-lines and W-lines, use the P-lines as reference paths.
  • Reference paths have sample name _gbwt_ref and the path name as contig name.
• GBWTGraph file format version 2.
  • Optional node-to-segment translation for GFA files.
  • Compatible with version 1.
• Preliminary SegmentHandleGraph interface for GBWTGraph.
  • If node-to-segment translation is included in the graph, each handle maps to a (segment name, starting offset) pair.
  • Each node also maps to a (segment name, node id range) pair.
  • Iteration over segments and links.
• Compressed GBWTGraph file format for GFA storage.
  • Both GBWT and GBWTGraph in the same file. GBWTGraph typically compresses to ~20% of the original space.
  • gfa2gbwt can output plain and compressed formats and convert between the two.
• GFA extraction from GBWTGraph.