Will complete this when updating to Vega 2.2.5 or newer, which
contains a new feature that I contributed specifically for this.

* 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.

* 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.

* 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.

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.

* 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.

* 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.

* 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.

* 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.