@starius starius released this Jun 12, 2015 · 380 commits to master since this release

Assets 8

Release 0.4.0

Improvements:

  • Change alignment requirements. Require high similarity in
    every slice of length MIN_LENGTH. Use logarithmic
    gap penalty. Introduce option MIN_END. Do not require
    length of fragment >= MIN_LENGTH.
  • Short blocks of one fragment are now called minor blocks.
    All minor blocks are shorter than MIN_LENGTH.
  • GUI/BSA: show block's length for global blocks.
  • Use Travis CI: https://travis-ci.org/npge/npge
  • BlockSet alignment: g-blocks and i-blocks. G-blocks
    are formed from joined consequent s-blocks. S-blocks
    are always aligned in g-blocks. Other blocks form
    i-blocks.
  • Speed up SplitRepeats. Improve time complexity by
    building the tree from diagnostic positions. Critical
    for blocks of > 500 fragments.
  • PostProcessing produces new files:
    • table of global blocks' properties (*.gbi)
    • blockset alignments with block names (*.blocks)
    • pangenome-small.bi
    • nj-global-tree-full.tre
    • genes/partition.tsv
  • Mutations file parser written in Python (example)
  • Print local time with timezone offset to logs
  • Add descriptions of some algorithms (*.md files)
  • Translate ECCB'14 abstract into Russian
  • Fix bugs:
    • Fix bugs in GUI
    • Fix bugs in annotations parser (GetData)
    • Fix bugs in local blockset alignment builder. It
      used to consider linear sequences to be circular.

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