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@vadimnazarov vadimnazarov released this 21 Aug 13:13
· 815 commits to master since this release

MAAG

1.0 version

  • Implement MAAG (Multi-Alignment Assembly Graph).
    • Implement full probability computing.
    • Implement slice probability computing.
    • Add a fix for joint VJ prob computing.
    • Add copy constructors for MAAG and MMC.
    • Implement forward-backward algorithm for VJ receptors.
      • Implement joint nucleotide distribution computing VJ receptors.
    • Implement forward-backward algorithm for VDJ receptors.
      • Implement joint nucleotide distribution computing VDJ receptors.
  • Implement MAAG builder.
    • Figure out MAAG builder interface.
    • Implement VJ MAAG builder.
    • Implement VDJ MAAG builder.
    • Optimise sizes of D deletions matrices.
    • Add a fix for joint VJ choosing.
    • Implement replaceEventProbabilities() function used for speed up statistical inference in models.
    • Pointers or copies in constructor?
      • Copies.
    • Figure out how to properly work with string iterators in insertions.
    • Check for 0-based or 1-based. All sequence building and other stuff should be 1-based, because it's the number of aligned characters.
    • Check edge cases, e.g., sequence positions vectors when all gene segment was deleted and insertions are inserted.

PAM

1.0 version

  • Change name from ASM to something like Probabilistic Assembling Model.
  • Add to ModelParameterVector joint VJ probabilities.
  • Refactor ModelParameterVector for easier access to event probabilities.
  • Implement basic PAM (probabilistic assembling model).
    • Implement model parameters reading from file procedure.
      • Add creating ModelParameterVector subroutine.
      • Add prob vector grow and shrink subroutines.
    • Implement computing probabiltiies procedure.
    • Implement clonotype assembler.
      • VJ
      • VDJ
    • Implement probabilities computing with recomputing the gene usage.
      • Implement
      • Test
    • Implement saving PAM's parameters to a file.
  • Implement Murugan EM algorithm.
  • Test EM algorithm and generation: generate an artificial repertoire and infer a model from it.
    • VJ
    • VDJ
  • Add test for D gene segment length in parsing prob data.
  • Add model parameter vector nulling procedure.
  • Think about the proper way to parse inputs.
    • Always default input for Ymir, external python script for parsing various formats.
      • tcR data frames.
      • MiTCR data frames

Other

1.0 version

  • Rename clones to clonotypes. (:
  • Add P-nucleotide making.
  • Add naive alignment step in the parser.
  • Implement a naive local aligner for Diversity genes.
  • Set up travis.
  • Add error messages to parser if some problems with gene segments has been found.
  • Add to parsers skip D alignment if genes are VJ.
  • Add skipping of empty lines at the ends of files to all parsers.
  • Add working drafts for default subroutines:
    • Computing.
      • C++ part.
      • Python 3 wrapper.
    • Inference.
      • C++ part.
      • Python 3 wrapper.
    • Generation.
      • C++ part.
      • Python 3 wrapper.
  • Check for 1-based option in converters;