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Documentation

• Data model: General | File formats
• Interface:
  • Global settings
  • Data types
  • Node / path identifiers
  • Construction: Direct construction | Merging | Removing sequences
  • Queries: Low-level queries | Searching | Cached GBWT
  • R-index locate structure
  • Haplotype generation
  • Metadata
• Benchmarks
• Version history
• Ideas that have not been implemented

Public interface

Everything is in namespace gbwt. Use linker option -lgbwt to link against the GBWT library.

• dynamic_gbwt.h: Construction interface
  • Includes gbwt.h
• cached_gbwt.h: Cached query interface
  • Includes gbwt.h
• fast_locate.h: R-index locate structure
  • Includes gbwt.h
• gbwt.h: Query interface
  • Includes algorithms.h
  • Includes files.h
  • Includes metadata.h
• algorithms.h: Search algorithms
  • Includes support.h
• variants.h: Support structures for haplotype generation
  • Includes utils.h
• files.h: File formats
  • Includes utils.h
• metadata.h: GBWT metadata
  • Includes support.h
• support.h: Support structures
  • Includes utils.h
• utils.h: Definitions and utility methods