1. 01 Sep, 2015 1 commit
    • 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 14 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Samplevis · 300549e0
      jhoogenboom authored
      * New visualisation Samplevis visualises sample data files.
        (Note: visualisations are currently stored in the package, but
        are not available via FDSTools commands yet. A new tool is going
        to be introduced later, which will copy the visualisation files
        to a user-selected folder.)
      * Including the current versions of Vega and D3 for completeness.
      * Fixed missing numpy dependency in setup.py.
      * Clarified some option help texts in Allelefinder based on
        feedback by Rick and Kris.
      300549e0