@starius starius released this Jan 13, 2016 · 204 commits to master since this release

Assets 8

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Warning. The installer and the program doesn't work from a directory with Russian letters in name.

@npge-bot npge-bot released this Nov 8, 2015 · 254 commits to master since this release

Assets 8

Release 0.5.2

Bug fixes.

  • Fix Windows build
    • Workaround for gcc5 bug
    • Disable LuaJIT explicitly
    • algo_lua.cpp: Lua 5.3 compatibility
    • fix windows build warning
  • Fix typos and errors in README and Info's output
  • config: do not fail with lua-npge npge.conf

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Warning. The installer and the program doesn't work from a directory with Russian letters in name.

Pre-release
Pre-release

@npge-bot npge-bot released this Oct 29, 2015 · 263 commits to master since this release

Assets 4

Release 0.5.1

Bug fixes and few improvements.

  • Pangenome: join collinear blocks even if bad.
  • Fix intermediate fragments joining. This bug was
    introduced in 2c76b51
    (2015-05-16), version 0.4.0 (2015-06-12).
  • Update requirements of a good pangenome in README.md
    according to what is implemented now.
  • Genes-vs-blocks partition: print only locus_tag.
  • GUI: jump to fragment end if there is no gene end.
  • Info: print % of NPG for total blocks length.
  • Recognize lua-npge format of Fragment id encoding.
  • Download compressed files from the database.
  • Fix errors in GetData and AddGenes.
  • AddGenes: skip repeated locus_tag.
  • Fix some build issues on various setups.
  • meta_test: ignore directories without script.npge.
  • Setup Travis for cross-compiling to Windows (MXE).
  • Setup Travis for uploading build artifacts to GitHub.
  • Update BLAST in the distribution to 2.2.31.

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Warning: the Windows build doesn't work! Please use Windows files from release 0.5.2.

@starius starius released this Jul 16, 2015 · 333 commits to master since this release

Assets 8

Release 0.5.0

Bug fixes and few improvements.

  • Change alignment requirements.
    • Change meaning and default value of MIN_END.
    • Add option FRAME_LENGTH.
  • Add processor CountSMS
  • Filter: increase size of gap score table to 1000
  • Tools.
    • BLAST version: 2.2.29 -> 2.2.30
    • Option npge -v [--version]
    • Clarify option -g
    • Hide option DEV_NULL from npge.conf
    • GUI: show % of length occupied by low similarity
    • Examine: do not recommend nan identity
  • Documentation.
    • ECCB'14: add abstract in English (original)
    • README: meaning of columns of *.bi files
    • README: add blocks types algorithm (image)
  • Fix bugs.
    • FreeBSD build fixes. Thanks to Dmitry Marakasov!
    • Fix segfault in PrintPartition.
    • Fix the bug in BlastFinder (crash on empty input).
    • Fix windows x64 build.
    • Do not apply UPX to 64-bit Windows executables.
    • Lua code: compatibility with Lua >= 5.2.
    • Find more locus_tag's in GeneBank files.
    • FindLowSimilar: fix division by zero.

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@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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