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. 10 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Finishing StuttermodelVis · 4eee1a33
      jhoogenboom authored
      * Properly implemented the options on the StuttermodelVis HTML
        visualisation.
      * Added filtering options for marker and repeat unit to
        StuttermodelVis.
      * Added StuttermodelVis to the Vis tool.
      
      General visualisation changes:
      * Updated Vega to v2.2.4.
      * Fixed glitch that caused mouseover events in HTML visualisations
        to stop working after the renderer was switched.
      * The file name suggested by the Save Image link in HTML
        visualisations is now derived from the name of the loaded data
        file.
      4eee1a33
  3. 01 Sep, 2015 2 commits
    • 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
    • jhoogenboom's avatar
      Various bug fixes and additions · ce7f34fb
      jhoogenboom authored
      Fixed:
      * Fixed crash that would occur when an empty sequence (primer dimer) is converted from raw to TSSV-style (or allelename) format.
      * Fixed bug in BGHomRaw that caused incorrect sample tags in the output.
      * Fixed bug that caused allele names with negative CE numbers and names of primer dimers to be regarded as 'invalid allele names' even though FDSTools generated those names itself.
      * Fixed crash when reading sample data while looking for an annotation column.
      * Fixed bug in Allelefinder resulting in the complete absence of output that occurred when a column name with Stuttermark output was specified.
      
      Changed:
      * Restyled the Options box on HTML visualisations. It is now less transparent and oriented more vertically to reduce overlap with the visualisation. Options are now presented in groups.
      * Updated Vega to version 2.2.1.
      
      New:
      * Added *_corrected columns to BGCorrect output for convenience. E.g., the total_corrected column contains the value of total-total_noise+total_add.
      * Added -L/--log-scale option to the Vis tool.
      ce7f34fb
  4. 26 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGRawVis · 8213ec14
      jhoogenboom authored
      * Added new visualisation BGRawVis to the Vis tool. It visualises BGHomRaw output data.
      * Now using more reliable linear X axis label formatting in Profilevis.
      * Changed filtering operands in Profilevis and Samplevis from > to >=.
      8213ec14
  5. 24 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Added Profilevis to the Vis tool and added various enhancements. · 513f967a
      jhoogenboom authored
      * Added options for the graph width and filtering on marker name to
        Samplevis and Profilevis.
      * The text fields in the HTML versions of Samplevs and Profilevis
        now update the graph OnChange instead of OnKeyUp. This is done
        because rendering the graph takes a while with large data files.
      * Fixed glitch in Profilevis that caused useless horizontal axis
        labels when the logarithmic scale is used.
      * Fixed glitch in Profilevis that caused Vega to render the graph
        even before data was loaded.
      * Changed -R option of SeqConvert to -r to avoid a potential
        collision with the -R/--report option if SeqConvert ever gets
        report output support in the future.
      513f967a
  6. 21 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Profilevis, and various bug fixes · b7d64a4f
      jhoogenboom authored
      * New visualisation Profilevis added to the package, but not yet to
        the Vis tool.
      * The Vis tool now prints a helpful error message if no output file
        was specified, instead of printing half a megabyte of HTML and
        minified JavaScript to the terminal.
      * Fixed crash that occurred when attempting to convert the sequence
        of an alias to its allele name.
      * Fixed various bugs in the functions that convert sequences to
        TSSV-style and allele names. Only the conversion of non-matching
        sequences was affected.
      * Added "max_expected_copies" section to the FDSTools library
        format. The default value is 2. Allelefinder will now use these
        as the maximum number of alleles per marker if the
        -a/--max-alleles option is not specified.
      * The section headers in the FDSTools library format are now case
        insensitive.
      b7d64a4f
  7. 18 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Vis · 2c96971b
      jhoogenboom authored
      * New tool Vis creates an interactive visualisation in HTML format,
        or a bare Vega graph spec (JSON format). The user can choose to
        supply a data file that will be embedded in the visualisation
        file. If no data file is given, the HTML visualisation will offer
        a file selection element, or the bare JSON output will refer to a
        file called 'data.csv'.
      * Changes to Samplevis:
        * The Options box can now be opened/closed.
        * Added options to change the width of the bars and the space
          between subgraphs (markers).
        * Added options to filter by read count or percentage vs the
          highest allele of the marker.
        * Replaced deprecated 'zip' data transforms in the Vega spec with
          the new 'lookup' transform.
      * Updated bundled Vega to v2.1.1.
      2c96971b