GBWTGraph v0.9

• Terminology change consistent with libhandlegraph senses:
  • Old reference paths are now generic (named) paths.
  • Some samples may be interpreted as reference paths.
  • All other paths are haplotype paths.
• GFA compression/decompression changes:
  • The output is GFA 1.1 instead of GFA 1.0.
  • Path names are now interpreted as contig names instead of sample names by default.
  • Preset --pan-sn for parsing path names and extracting paths in the PanSN format.
  • --ref-only mode that extracts only graph topology and named paths as P-lines.
  • An optional list of reference samples can be stored using GFA header tag RS and GBWT tag reference_samples.
  • The API supports multiple regexes for parsing path names and assigning path senses by the first regex that matches the path name.
• GBWTGraph implements the PathMetadata interface from libhandlegraph.
  • Metadata that depends on the sense (type) of the path.
  • Haplotype paths are not exposed through the PathHandleGraph interface.
• Construction from HandleGraph takes an optional NamedNodeBackTranslation for building the node-to-segment translation.
• Path cover / subsampled GBWTs now include (a selected subset of) paths from the original graph as generic paths.