• Hoogenboom, Jerry's avatar
    Big update: Bumped version to v0.0.3 · ebf700a7
    Hoogenboom, Jerry authored
    Updated Stuttermark to v1.5. WARNING: This version of Stuttermark is
    INCOMPATIBLE with output from previous versions of FDSTools and TSSV.
    
    Introducing TSSV-Lite
    * New tool tssv acts as a wrapper around TSSV-Lite (tssvl). Its primary
      purpose is to allow running TSSV-Lite without having to convert the
      FDSTools library to TSSV format, and to offer allelename output. Like
      all other tools in FDSTools, it also works with TSSV library files but
      its allele name generation capabilities are limited in that case.
    
    Changed:
    * TSSV-Lite and the new TSSV tool in FDSTools have two columns renamed
      w.r.t. the original TSSV program: 'name' has been changed to 'marker',
      and 'allele' has been changed to 'sequence'. All tools in FDSTools
      have been updated to use the new column names. This change affects
      Allelefinder, BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict,
      Blame, Samplestats, Samplevis, Stuttermark, Stuttermodel, and
      Seqconvert. Note that this change will BREAK COMPATIBILITY of these
      tools with old data files.
    
    Fixed:
    * In Samplevis HTML visualisations, the "percentage recovery" table
      filtering option used the absolute number of recovered reads instead.
    * Added PctRecovery to the tables in Samplevis HTML visualisations.
    * BGPredict will now print a nice error message if the -n/--min-pct
      option is set to zero or a negative number, to avoid division by zero.
    * Samplestats would crash if the input file contained the flags column.
    * FDSTools would crash when trying to convert sequences to allele names
      using a TSSV library.
    
    Improved:
    * Libconvert will no longer include duplicate sequences in the STR
      defenition when converting to TSSV format and the reference sequence
      of one of the markers is the same as one of its aliases, or when
      aliases of one marker share one or more prefix or suffix sequences.
    * Updated add_input_output_args() such that the output file is a
      positional argument (instead of -o) for tools that have a single input
      file and no support for batches.
    * Updated add_sequence_format_args() such that the library file can be
      made a required argument.
    * Refined the FDSTools package description, since FDSTools does more
      than just noise filteirng.
    * FDSTools will now do a marginally better job at producing allele names
      for sequences that do not exactly match the provided STR pattern. When
      seeking the longest matching portion of the sequence, it will now also
      test the reversed sequence with a reversed pattern, which sometimes
      yields a longer match. It is still not optimal, though, but some
      refactoring has been done to move away from regular expressions.
    * BGCorrect will now also fill in correction_flags for newly added
      sequences.
    * Adjusted the help text of Samplestats to include the fact that the -c
      and -y options have an OR relation instead of an AND relation.
    * BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict, and
      Stuttermodel will now ignore special values that may appear in the
      place of a sequence (currently: 'Other sequences' and 'No data').
    
    Removed:
    * The -m/--marker-column and -a/--allele-column arguments of BGPredict
      had no effect and have been removed.
    
    Visualisations:
    * Updated bundled D3 to v3.5.12.
    * In HTML visualisations, if the page is scrolled to the right edge when
      an option is changed that causes the graphs to become wider, the page
      now remains scrolled to the right.
    * Samplevis HTML visualisations:
      * Added 'Clear manually added/removed' link to the table filtering.
      * Reduced flicker of the mouse cursor in Internet Explorer.
      * Added 'Common axis range' checkbox (only available when 'Split
        markers' is off).
      * Added 'Save table' link to save the table of selected alleles to a
        tab-separated file.
      * Added 'PctRecovery' column to the tables of selected alleles.
      * An alert box is now shown when a data file is loaded that contains
        markers that have 'No data'.
      * Added 'Percentage of total reads' to the graph filtering options.
      * Added a note to the table filtering options to explain that the
        minimum percentage correction and recovery have an OR relation.
    ebf700a7
bgestimate.py 21 KB