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GBWTGraph v1.0

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@jltsiren jltsiren released this 05 Dec 04:02
· 41 commits to master since this release

Things have stabilized enough to call this version 1.0. It contains a number of changes from the last year and a half.

  • Faster copying / moving / swapping of GBZ objects.
  • GFA compression/decompression changes:
    • L-line overlap is now written as 0M instead of *.
    • Option to extract GFA without using the node-to-segment translation.
  • Minimizer index version 9:
    • Payload is now 128 bits per hit (already in version 8).
    • Parameterized over both key type and value type, allowing the use minimizer indexes without a payload.
    • Option to provide a set of frequent kmers that should be avoided as minimizers, as in Winnowmap.
    • Plain kmer indexes can also be used.
    • Iterator over the kmers in the index.
    • Compatible with version 8 but not with earlier versions.
  • New graph operations:
    • subgraph(): Return a subgraph based on the given GBWT index (faster than using a constructor).
  • New algorithms:
    • gbwt_construction_jobs(): Partition a graph into sets of components for parallel GBWT construction.
    • partition_chains(): Partition top-level chains in a snarl decomposition between GBWT construction jobs.