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.

* 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.

* 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.

* All tools now write to stdout by default. Tools that support
  writing report files write those to stderr by default. The
  -o/--output and -r/--report options can be used to override
  these.
* Tools that operated on one sample at a time (bgcorrect,
  seqconvert, stuttermark) now support batch processing. The new
  -i/--input argument takes a list of files. In batch mode,
  the -o/--output argument can be used to specify a list of
  corresponding output files (which must be the same length). It
  is also possible to specify a format string to automatically
  generate file names. -o/--output defaults to "\1-\2.out" which is
  automatically expanded to "sampletag-toolname.out". The old
  positional arguments [IN] and [OUT] are maintained and allow for
  conveniently running the tools on a single sample file.
  [IN] is mutually exclusive with -i/--input and [OUT] is mutually
  exclusive with -o/--output. [OUT] now also accepts the filename
  format, but when not in batch mode, it still defaults to stdout.
  Note that by default, the sample tag is extracted from the input
  filenames by simply stripping the extension. This means a minimal
  batch processing command like "fdstools stuttermark -i *.csv"
  automatically creates a "...-stuttermark.out" file next to each
  CSV file in the current working directory.
* Libconvert now also supports only specifying an output file.
  This makes it easier to write the default FDSTools library to a
  new file. E.g., "fdstools libconvert mynewfile.txt" now creates
  "mynewfile.txt" if it does not exist, and writes the default
  library to it. Most helpful.

* All tools now have a longer description in the tool-specific help
  page.
* Arguments are now presented in groups and the order is the same
  across tools.

Furthermore:
* Fixed bug that rendered BGHomStats and BGEstimate with the -H
  option useless.
* The report of Allelefinder and BGEstimate is now written to
  sys.stderr by default. This means the report is now always
  generated (but it may be sent directly to /dev/null explicitly by
  the user). The big plus is that the progress of the tools is
  visible in the terminal when the tools are run by hand.

* New tool Blame can be used to find particularly dirty samples and
  to construct a DNA profile of the contaminator.
* Fixed bug BGCorrect that resulted in incorrect values in the
  *_add columns.
* BGEstimate and BGHomStats no longer crash if a library file is
  provided.
* SeqConvert can now use a different library file for the output,
  thereby offering some possibilities to update allele names when a
  library file gets updated.
* Replaced various uses of map() by generator expressions and
  listcomps for increased readability speed (although slightly).

* Added BGCorrect tool for filtering noise in case samples.
* BGEstimate now writes its output in tab-separated format, instead
  of JSON.
* Small changes to help output formatting.