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odgi 0.6 - Domani
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@AndreaGuarracino AndreaGuarracino released this 16 Jun 09:51
· 1005 commits to master since this release
0.6
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Buildable Source Tarball: odgi-0.6.tar.gz

This release includes:

  • new commands:
    • odgi position: find, translate, and liftover graph and path positions between graphs;
    • odgi extract: extract subgraphs or parts of a graph defined by query criteria;
    • odgi explode: breaks a graph into connected components storing each component in its own file;
    • odgi squeeze: squeezes multiple graphs into the same file;
    • odgi depth: find the depth of a graph as defined by query criteria;
    • odgi degree: describe the graph in terms of node degree;
    • odgi validate: validate a graph checking if the paths are consistent with the graph topology;
    • odgi overlap: find the paths touched by given input paths.
  • bug fixes and performance improvements in several commands (odgi unchop included). The focus was on parallelization to scale on gigabase-scale pangenome graphs.
  • the documentation has been given a major overhaul, including detailed tutorials for different biological application cases. The Docs are hosted permanently at https://odgi.readthedocs.io/en/latest/index.html.
  • uniformed and beautified command-line options. All options are now organized in groups and mandatory arguments are highlighted.
  • usage of jemalloc as a new memory allocator to tackle memory fragmentation and support scalable concurrency.
  • odgi bin can emit output formatted for HaploBlocker.
  • new statistics in odgi stats (separated connected components, self-loop, nondeterministic-edges).
  • new layout initialization in odgi layout.
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