1. 04 Nov, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Implemented support for non-STR markers, improved file handling and more · 1083919c
      Hoogenboom, Jerry authored
      Additions and improvements to the FDSTools library file format:
      * New [genome_position] section in FDSTools-style library files allows
      for specifying the chromosome and position of each marker.
      * New [no_repeat] section in FDSTools-style library files allows for
      including non-STR markers.
      * Comma/semicolon/space-separated values in FDSTools-style library files
      can now also be separated by tab characters and multiple consecutive
      separators are no longer collapsed (with the exception of whitespace).
      * If no prefix and/or suffix has been specified for an alias, the
      prefix/suffix of the marker itself is used.
      * Implemented support for non-STR markers (e.g. SNP clusters) and mtDNA
      markers. Allele names of the latter follow mtDNA nomenclature.
      * Improved the logic of generating STR allele names for sequences that
      have a prefix or suffix sequence that was not included in the library
      file.
      * Updated and clarified various explanatory texts in generated FDSTools
      library files.
      
      Fixed:
      * Fixed a bug that caused prefix/suffix variants in aliases to go
      missing in allele names.
      
      Improved file handling:
      * Library files are now closed immediately after parsing them.
      * Sample data input files are opened one at a time now.
      
      Visualisations:
      * Updated Vega to version 2.3.1.
      * Worked around a bug in Google Chrome that caused the 'Save image' link
      to stop working after having been used once.
      1083919c
  2. 03 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Introducing StuttermodelVis (not complete yet) · e0eef88d
      jhoogenboom authored
      * Added StuttermodelVis HTML file and JSON spec. The rendering
        works, but some of the options are not implemented yet. It is
        also not yet added to the Vis tool.
      * Changed the order of stuttermodel's coefficients: 'a' used to be
        the most significant coefficient, now it is the least significant
        coefficient (the shift). The benefit of this is that when moving
        to higher-order polynomials, the extra coefficients do not change
        the meaning of the others. So 'a' is now always the shift, 'b' is
        the linear component, 'c' the quadratic, etc.
      * Added some development notes (including todo list) that I had
        kept outside of the project until now.
      e0eef88d
  3. 01 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Cleanup and minor enhancements · 03fc3d49
      jhoogenboom authored
      * BGCorrect and Stuttermark will now exit with an error message if
        more than one input file for the same sample is specified and no
        separate output files are given. Previously these tools would
        just overwrite the output file repeatedly, discarding the output
        of all but the last data file of the sample.
      * Removed to main() functions and related stubs from the tools
        because they are not actually runnable directly anyway.
      * Added some more help text to some of the tools.
      * Doubled the size of the marker name filter input element on the
        HTML visualisations.
      03fc3d49
  4. 12 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGMerge · 6207d485
      jhoogenboom authored
      * New tool BGMerge can be used to merge background noise profiles
        (e.g., merge BGPredict output with a database previously
        obtained from BGEstimate).
      * Fixed two major bugs in BGPredict that resulted in incorrect fit
        functions being used.
      * BGEstimate, BGPredict, BGHomStats, Blame, and StutterModel no
        longer crash if a library file is specified.
      * Added reverse strand profile estimation to BGPredict.
      6207d485
  5. 11 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGPredict · 276a0439
      jhoogenboom authored
      * New tool BGPredict predicts background noise profiles (containing
        only stutter products) for user-supplied alleles/sequences using
        a trained stutter model obtained from Stuttermodel. Currently
        only the amounts of the forward strand are predicted.
      * New option -L/--min-lengths for Stuttermodel allows to set a
        minimum required number of unique repeat lengths to base the
        fits on (default: 5).
      * Updated formatting of output of Stuttermodel: added '+' sign to
        positive stutter, limited r2 scores to 3 decimal places, and now
        all coefficients are written in scientific notation with 3
        decimal places.
      * The --output-column option of SeqConvert now defaults to using
        the value of --allele-column.
      276a0439