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@maxibor maxibor released this 21 Apr 14:58
· 49 commits to master since this release
1.0.0-beta
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Learn about vigilant mode.

Changelog

Added

  • Added sam2lca tutorial
  • Add Custom acc2tax with json
  • Total number of reads is computed early on to provide progress bar
  • unit and integration testing with PyTest
  • Total Descendant read counts for each taxon
  • GTDB taxonomy and acc2tax added
  • 18s acc2tax added
  • XN and XR flag in bam output for, respectively, Taxon name and rank
  • Add edit distance threshold filtering
  • JOSS article

Changed

  • Code refactoring for speedup, making use of multithreading on shared dictionaries
  • Improve logging and replace prints statements with logging.info
  • ete3 has been replaced by taxopy
  • Unclassified TAXID is now 12908 by default
  • RocksDB params changed
  • TAXID of LCA is only attributed to alignment segments passing threshold
  • Identity threshold is now a range selection in CLI.

Dependencies

  • ete3 removed
  • ordered-set removed
  • pytest-console-scripts 1.3.1
  • scipy
  • Jinja2 pinned version ot 3.1 (see RTD issue )
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