* General changes in v1.1.0.dev3:
  * Allele name heuristics: don't produce insertions at the end of the
    prefix or at the beginning of the suffix; just include extra STR
    blocks.
  * FDSTools will no longer crash with a 'column not found' error when
    an input file is empty. This situation is now treated as if the
    expected columns existed, but no lines of actual data were present.
    This greatly helps in tracking down issues in pipelines involving
    multiple tools, as tools will now shutdown gracefully if an upstream
    tool fails to write output.
* Allelefinder v1.0.1:
  * Fixed crash that occurred when converting sequences to allele names
    format while no library file was provided.
  * Don't crash when output pipe is closed.
* BGAnalyse v1.0.1:
  * Don't crash when output pipe is closed.
* BGCorrect v1.0.2:
  * Don't crash on empty input files.
  * Don't crash when output pipe is closed.
* BGEstimate v1.1.2:
  * Don't crash when output pipe is closed.
* BGHomRaw v1.0.1:
  * Clarified the 'Allele x of marker y has 0 reads' error message with
    the sample tag.
  * Don't crash when output pipe is closed.
* BGHomStats v1.0.1:
  * Error messages about the input data now contain the sample tag of
    the sample that triggered the error.
  * Don't crash when output pipe is closed.
* BGMerge v1.0.3:
  * Don't crash when output pipe is closed.
* BGPredict v1.0.2:
  * Don't crash on empty input files.
  * Don't crash when output pipe is closed.
* FindNewAlleles v1.0.1:
  * Don't crash on empty input files.
  * Don't crash when output pipe is closed.
* Libconvert v1.1.2:
  * Don't crash when output pipe is closed.
* Library v1.0.3:
  * Don't crash when output pipe is closed.
* Seqconvert v1.0.2:
  * Don't crash when output pipe is closed.
* Samplestats v1.1.1:
  * Don't crash on empty input files.
  * Don't crash when output pipe is closed.
* Stuttermark v1.5.1:
  * Don't crash on empty input files.
  * Don't crash when output pipe is closed.
* Stuttermodel v1.1.2:
  * Don't crash when output pipe is closed.
* TSSV v1.1.0 (additionally):
  * When running analysis in parallel, make tasks of 1 million alignments.
    Previously, this was 10k reads, with the number of alignments per task
    depending on the size of the library file. This caused memory issues for
    huge libraries like whole mt interval libraries.
  * Don't crash when output pipe is closed.
* Vis v1.0.4:
  * Don't crash when output pipe is closed.

* General changes in v1.0.1:
  * Fixed crash that occurred when using the -i option to run the same command
    on multiple input files.
  * The usage string now always starts with 'fdstools', even if FDSTools was
    invoked using some other command (e.g. on Windows, FDSTools gets invoked
    through a file called 'fdstools-script.py').
  * Fixed bug with the -d/--debug option being ignored if placed before the
    tool name on systems running Python 2.7.9 or later.
  * FDSTools library files may now contain IUPAC ambiguous bases in the
    prefix and suffix sequences of STR markers (except the first sequence,
    as it is used as the reference).  Additionally, optional bases may be
    represented by lowercase letters.
  * If no explicit prefix/suffix is given for an alias, the prefix/suffix of
    the corresponding marker is assumed instead. This situation was not
    handled correctly when converting from raw sequences to TSSV or allelename
    format, which resulted in the alias remaining unused.
* Stuttermodelvis v2.0.2:
  * Added filtering option for the stutter amount (-1, +1, -2, etc.).
  * Added filtering option for the coefficient of determination (r squared
    value) of the fit functions.
* Libconvert v1.1.1:
  * Adjustments for supporting IUPAC notation in prefix and suffix sequences
    when converting from FDSTools to TSSV library format.
* Library v1.0.2:
  * Added documentation for IUPAC support to the descriptive comment of the
    [prefix] section.

* General changes in v1.0.0rc1:
  * Fixed bug that caused variant descriptions in allele names of
    non-STR markers to be prepended with plus signs similar to suffix variants
    in STR markers.  When attempting to convert these allele names back to raw
    sequences, FDSTools would crash with an 'Invalid allele name' error.
* Allelevis v2.0.1 (additionally):
  * In the tooltip in HTML visualisations, a line break may now only be
    inserted in allele names after an underscore character (_) or after a
    repeat block in STR allele names.  If the input file contains raw
    sequences, line breaks may now be introduced anywhere in the sequence.
* Samplevis v2.1.1:
  * Added tooltip support to HTML visualisations.  Moving the mouse pointer
    over one of the alleles in the graph now displays a tooltip giving
    per-strand read counts of that allele.  The tooltip may include a
    'new allele' note if the input sample was analysed with FindNewAlleles.
  * The allele tables in HTML visualisations will now grow much wider than
    before if the screen (or window) is very narrow.
  * In the tables in HTML visualisations, a line break may now only be inserted
    in allele names after an underscore character (_) or after a repeat block
    in STR allele names.  If the input file contains raw sequences, line breaks
    may now be introduced anywhere in the sequence.
  * Improved determination of column widths of the allele tables when printing
    an HTML visualisation.
  * When printing an HTML visualisation, the graph and the corresponding table
    of a marker will be kept on the same page in all browsers now.
  * Fixed glitch that caused 'Infinity%' or 'NaN%' to be written in some cells
    in the allele tables in HTML visualisations for sequences that had zero
    reads (before or after correction).  These cells will remain empty now.
* Pipeline v1.0.1 (additionally):
  * The Pipeline tool will now only write the command lines of the tools it
    runs if the -d/--debug option was specified.
* Library v1.0.1 (additionally):
  * Added proper examples for non-STR markers and aliases.
* Stuttermodel v1.1.1:
  * Minor change to internal variant representation.

* General changes in v0.0.6.dev1:
  * Tools that take a list of files as their argument (through the -i option or
    as positionals) now explicitly support glob patterns.  This means they will
    interpret '*' and '?' characters as wildcards for 'zero or more characters'
    and 'any one character', respectively.  On Unix-like systems this is
    generally done by the shell, but on Windows one had to specify every file
    name completely.
* BGEstimate v1.1.1:
  * Added option -p/--profiles which can be used to provide a previously
    created background noise profiles file.  BGEstimate will read starting
    values from this file instead of assuming zero noise.
* BGMerge v1.0.2:
  * Small code changes to facilitate explicit glob pattern matching support.
* Pipeline v1.0.1:
  * The Pipeline tool will no longer check the existence of the files specified
    for the -S/--in-samples option; instead, this is left to the downstream
    tools to find out, consistent with how this works with the other input file
    options.
* Allelevis v2.0.1:
  * Added tooltip support to HTML visualisations.  Moving the mouse pointer
    over a node or edge in the graph now displays a tooltip giving allele names
    and sample counts.
* Stuttermodelvis v2.0.1:
  * Changed the unit in the horizontal axis title from 'bp' to 'nt'.
* Library v1.0.1:
  * Updated some of the comments describing the sections.

* General changes in v0.0.5:
  * The TSSV tool now depends on version 0.4.0 of TSSV.
  * Added new Pipeline tool that runs one of three default analysis pipelines
    automatically given a configuration file with tool options and input/output
    file names. The three available pipeline options are 'reference-sample',
    analysing a single reference sample with TSSV and Stuttermark;
    'reference-database', analysing a collection of reference samples with
    BGEstimate and Stuttermodel; and 'case-sample', analysing a single case
    sample with TSSV, BGPredict, BGMerge, BGCorrect, and Samplestats.
  * Added new Library tool that creates an empty FDSTools library file. Users
    may optionally specify the intented use of the library (STR markers,
    non-STR-markers, or both). Only the sections that apply to the given types
    of markers will be included in the output. The [aliases] section is not
    included by default, but an option is available to add it.
  * Added new tool BGAnalyse which can be used to analyse the remaining amount
    of noise in reference samples after correction.  This tool is a more
    sensitive successor of the 'Blame' tool.
  * Added new visualisation BGAnalysevis for visualising data obtained from
    BGAnalyse. This visualisation allows for identifying unclean or otherwise
    suboptimal samples by comparing the lowest, highest, and/or total remaining
    noise after correction for each marker in each sample.
  * The Blame tool was removed in favour of BGAnalyse.
* Libconvert v1.1.0:
  * When converting to FDSTools format, Libconvert automatically creates an
    empty FDSTools library file with the same contents as what would be
    obtained from the new Library tool without arguments.
  * The -a/--aliases option was modified such that it has the same effect as
    the -a/--aliases option of the new Library tool. This means that without
    this option specified, the [aliases] section will not be present in the
    output anymore.
  * The ability of the Libconvert tool to produce an empty FDSTools library
    file if no input file was given has been removed from the documentation
    (but not from the tool itself).
* TSSV v1.0.2:
  * Added new option -n/--indel-score which can be used to increase the
    penalty given to insertions and deletions in the flanking sequences w.r.t.
    the penalty given to mismatches.
  * NOTE: Requires TSSV v0.4.0 or newer to be installed.
* Vis v1.0.2:
  * Changed default value of -n/--min-abs from 15 to 5.
  * Added -I/--input2 option, which allows for specifying a file with raw data
    points for Stuttermodelvis and Profilevis.
  * Added support for creating BGAnalysevis visualisations.
* Profilevis v2.0.0:
  * Replaced the simple Options overlay with responsive design options panels
    in HTML visualisations.
  * Alleles and sequences are now sorted by CE allele length when applicable.
  * Added option to plot BGHomRaw data on top of the profiles.
  * Added marker selection menu for easier filtering.
* BGRawvis v2.0.0:
  * Replaced the simple Options overlay with responsive design options panels
    in HTML visualisations.
  * Sequences are now sorted by CE allele length when applicable.
  * Changed default minimum number of reads from 15 to 5.
  * Added marker selection menu for easier filtering.
* Stuttermodelvis v2.0.0:
  * Replaced the simple Options overlay with responsive design options panels
    in HTML visualisations.
  * Fixed glitch that caused the graphs to be re-rendered twice when loading
    a file by drag-and-drop in HTML visualisations.
  * Fixed glitch that made it possible to replace the data that was embedded
    in an HTML visualisation through drag-and-drop.
  * Added repeat unit selection menu for easier filtering.
* Allelevis v2.0.0:
  * Replaced the simple Options overlay with responsive design options panels
    in HTML visualisations.
  * Reduced Vega graph spec complexity by using the new Rank transform to
    position the subgraphs.
  * Fixed glitch that caused unnecessary padding around the graph.
* Samplestats v1.1.0:
  * Changed default allele calling option thresholds:
    * Changed default value of -m/--min-pct-of-max from 5.0 to 2.0.
    * Changed default value of -p/--min-pct-of-sum from 3.0 to 1.5.
  * Mentioned allele calling in the tool descriptions.
* Samplevis v2.1.0:
  * Changed default minimum number of reads for graph filtering from 15 to 5.
  * Changed default table filtering options:
    * Percentage of highest allele per marker changed from 5% to 2%.
    * Percentage of the marker's total reads changed from 3% to 1.5%.
    * Minimum number of reads in both orientations changed from 0 to 1.

* Global changes in v0.0.4:
  * FDSTools will now print profiling information to stdout when the -d/--debug
    option was specified.
  * Fixed bug where specifying '-' as the output filename would be taken
    literally, while it should have been interpreted as 'write to standard out'
    (Affected tools: BGCorrect, Samplestats, Seqconvert, Stuttermark).
  * Added more detailed license information to FDSTools.
* BGEstimate v1.1.0:
  * Added a new option -g/--min-genotypes (default: 3). Only alleles that occur
    in at least this number of unique heterozygous genotypes will be
    considered. This is to avoid 'contamination' of the noise profile of one
    allele with the noise of another. If homozygous samples are available for
    an allele, this filter is not applied to that allele. Setting this option
    to 1 effectively disables it. This option has the same cascading effect as
    the -s/--min-samples option, that is, if one allele does not meet the
    threshold, the samples with this allele are excluded which may cause some
    of the other alleles of these samples to fall below the threshold as well.
* Stuttermodel v1.1.0:
  * Stuttermodel will now only output a fit for one strand if it could also
    obtain a fit for the other strand (for the same marker, unit, and stutter
    depth). This new behaviour can be disabled with a new -O/--orphans option.
  * Fixed bug that caused Stuttermodel to output only the raw data points for
    -1 and +1 stutter when normal output was supressed.
* BGCorrect v1.0.1:
  * Added new column 'weight' to the output. The value in this column expresses
    the number of times that the noise profile of that allele fitted in the
    sample.
* Samplestats v1.0.1:
  * Samplestats will now round to 4 or 5 significant digits if a value is
    above 1000 or 10000, respectively. Previously, this was only done for the
    combined 'Other sequences' values.
  * The 'Other sequences' lines will now also include values for
    total_recovery, forward_recovery, and reverse_recovery.
  * The total_recovery, forward_recovery, and reverse_recovery columns are no
    longer placed to the left of all the other columns generated by
    Samplestats.
  * The help text for Samplestats erroneously listed the X_recovery_pct instead
    of X_recovery.
  * Added support for the new 'weight' column produced by BGCorrect when the
    -a/--filter-action option is set to 'combine'.
* BGPredict v1.0.1:
  * Greatly reduced memory usage.
  * BGPredict will now output nonzero values below the threshold set by
    -n/--min-pct if the predicted noise ratio of the same stutter on the other
    strand is above the threshold. Previously, values below the threshold were
    clipped to zero, which may cause unnecessarily high strand bias in the
    predicted profile.
* BGMerge v1.0.1:
  * Reduced memory usage.
* TSSV v1.0.1:
  * Renamed the '--is_fastq' option to '--is-fastq'. It was the only option
    with an underscore instead of a hyphen in FDSTools.
  * Fixed crash that would occur if -F/--sequence-format was set to anything
    other than 'raw'.
* Libconvert v1.0.1:
  * Specifying '-' as the first positional argument to libconvert will now
    correctly interpret this as "read from stdin" instead of throwing a "file
    not found" error (or reading from a file named "-" if it exists).
* Seqconvert v1.0.1:
  * Internal naming of the first positional argument was changed from 'format'
    to 'sequence-format'. This was done for consistency with the
    -F/--sequence-format option in other tools, giving it the same name in
    Pipeline configuration files.
* Vis v1.0.1:
  * Added -j/--jitter option for Stuttermodelvis (default: 0.25).
  * Vis would not allow the -n/--min-abs and the -s/--min-per-strand options to
    be set to 0.
* Stuttermodelvis v1.0.0beta2:
  * HTML visualisations now support drawing raw data points on top of the fit
    functions. The points can be drawn with an adjustable jitter to reduce
    overlap.
  * Fixed a JavaScript crash that would occur in HTML visualisations if the
    Repeat unit or Marker name filter resulted in an invalid regular expression
    (e.g., when the entered value ends with a backslash).
  * Reduced Vega graph spec complexity by using the new Rank transform to
    position the subgraphs.
  * HTML visualisations made with the -O/--online option of the Vis tool will
    now contain https URLs instead of http.
* Samplevis v1.0.1:
  * Fixed a JavaScript crash that would occur in HTML visualisations if the
    Marker name filter resulted in an invalid regular expression (e.g., when
    the entered value ends with a backslash).
  * Reduced Vega graph spec complexity by using the new Rank transform to
    position the subgraphs.
  * Fixed a glitch where clicking the 'Truncate sequences to' label would
    select the marker spacing input.
  * The 'Notes' table cells with 'BGPredict' in them now get a light orange
    background to warn the user that their background profile was computed.
    If a sequence was explicitly 'not corrected', 'not in ref db', or
    'corrected as background only', the same colour is used.
  * The message bar at the bottom of Samplevis HTML visualisations will now
    grow no larger than 3 lines. A scroll bar will appear as needed.
  * HTML visualisations made with the -O/--online option of the Vis tool will
    now contain https URLs instead of http.
* BGRawVis v1.0.1:
  * Fixed a JavaScript crash that would occur in HTML visualisations if the
    Marker name filter resulted in an invalid regular expression (e.g., when
    the entered value ends with a backslash).
  * Reduced Vega graph spec complexity by using the new Rank transform to
    position the subgraphs.
  * HTML visualisations made with the -O/--online option of the Vis tool will
    now contain https URLs instead of http.
* Profilevis v1.0.1:
  * Fixed a JavaScript crash that would occur in HTML visualisations if the
    Marker name filter resulted in an invalid regular expression (e.g., when
    the entered value ends with a backslash).
  * Reduced Vega graph spec complexity by using the new Rank transform to
    position the subgraphs.
  * HTML visualisations made with the -O/--online option of the Vis tool will
    now contain https URLs instead of http.
* Allelevis v1.0.0beta2:
  * Fixed potential crash/corruption that could occur with very unfortunate
    combinations of sample names and marker names.
  * HTML visualisations made with the -O/--online option of the Vis tool will
    now contain https URLs instead of http.
  * Added two more colours to the legend, such that a maximum of 22 markers is
    now supported without re-using colours.
* Updated bundled D3 to v3.5.17.
* Updated bundled Vega to v2.6.0.

Fixed:
* The -c/--stuttermark-column option of Allelefinder was not filtering
  out the non-ALLELE sequences as it was supposed to. (This issue was
  introduced in ce7f34fb, in which a bug was fixed that caused this
  option to filter all sequences, including the ones marked with ALLELE.
  So it turns out this option has been broken since 732e83ba.)

Improved:
* Allelefinder will no longer reject a marker based on the number of
  reads of 'Other sequences'.
* Adjusted sequence alignment parameters for mtDNA sequences to produce
  allele names that more closely follow historical mtDNA mutation
  nomenclature.

FDSTools would sometimes produce suboptimal alignments. Most notably, it
it would produce multiple smaller insertions/deletions when the
difference between two sequences could be described by one larger
insertion/deletion in combination with a base substitution. The latter
description is often more biologically sound and also usually results in
a shorter allele name.

* Fixed a bug that sometimes caused FDSTools to choose an incorrect path
  through the alignment matrix, producing a suboptimal alignment.
* Tweaked the alignment parameters to produce more meaningful results.

Added:
* Added a new section expected_allele_length to the FDSTools library
  format. In this section, the minimum and (optionally) maximum allele
  length of each marker can be specified.
* Added -L/--check-length option to the TSSV tool. If specified, the
  tool will use the expected_allele_length values to filter the results.
* Samplevis can now truncate long allele names to a given number of
  characters (defaulting to 70).
* Added an option to Samplestats to keep negatives when filtering (abs
  filter).

Changed:
* Renamed the --aggregate-below-minimum option of the TSSV tool to
  --aggregate-filtered.

Improved:
* Added an option to read_sample_data_file such that other code can
  request or require that the X_corrected columns are used.
* Samplestats will now round to 4 or 5 significant digits if a value is
  above 1000 or 10000, respectively.
* BGHomRaw will no longer round the forward, reverse, and total columns.
* When generating mtDNA allele names, FDSTools will now try to avoid
  creating gaps in the alignment of the sequences against the reference.
* Grouped the filtering options of the TSSV tool in its help text.
* Cleaned up some leftover code for special sequence value handling
  (more specifically: code that expected ensure_sequence_format to
  return False for special sequence values, which it no longer does).
* Cleaned up some dead legacy code in reduce_read_counts.

New tool findnewalleles:
* Given a list of known sequences, this tool can go through sample data
  files to mark all sequences that are not on the list.

Fixed:
* BGHomRaw, BGEstimate, BGHomStats, Stuttermodel, and Blame did not
  ignore the 'Other sequences' and 'No data' values that may occur in
  the place of a sequence as they were supposed to.

Improved:
* BGHomRaw will now include the sample tag in the "Missing allele X of
  marker Y" error message.
  
Changed:
* The -F/--sequence-format argument from BGHomRaw now defaults to "raw".

Visualisations:
* Updated Vega to version 2.5.0.
* The new version of Vega allowed the sorting to be fixed in Samplevis,
  Profilevis, BGRawvis, and Stuttermodelvis.
* Samplevis:
  * The 'Other sequences' bars are now drawn with an outline only.
  * STR alleles are now sorted by allele length by default (this can be
    toggled with a checkbox in HTML visualisations, and with an option
    in the Vis tool).
  * Fixed the clipping of the start of long allele names when printing
    SVGs from Google Chrome.
  * Added a note (as '?' help tooltip) to the Common axis range option
    in the HTML visualisation, to inform the user of the fact that the
    Split markers option needs to be off for it to work.

Improved:
* Added -A/--aggregate-below-minimum option to the TSSV tool. This will
  add a line with 'Other sequences' to the output summing all sequences
  that were not reported because they had less reads than was specified
  with the -a/--minimum option.
* Clarified the help text for the -D/--dir option of the TSSV tool.

Fixed:
* Updated all tools to consistently handle cases where 'No data' or
  'Other sequences' occurs in place of a sequence.

Updated Stuttermark to v1.5. WARNING: This version of Stuttermark is
INCOMPATIBLE with output from previous versions of FDSTools and TSSV.

Introducing TSSV-Lite
* New tool tssv acts as a wrapper around TSSV-Lite (tssvl). Its primary
  purpose is to allow running TSSV-Lite without having to convert the
  FDSTools library to TSSV format, and to offer allelename output. Like
  all other tools in FDSTools, it also works with TSSV library files but
  its allele name generation capabilities are limited in that case.

Changed:
* TSSV-Lite and the new TSSV tool in FDSTools have two columns renamed
  w.r.t. the original TSSV program: 'name' has been changed to 'marker',
  and 'allele' has been changed to 'sequence'. All tools in FDSTools
  have been updated to use the new column names. This change affects
  Allelefinder, BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict,
  Blame, Samplestats, Samplevis, Stuttermark, Stuttermodel, and
  Seqconvert. Note that this change will BREAK COMPATIBILITY of these
  tools with old data files.

Fixed:
* In Samplevis HTML visualisations, the "percentage recovery" table
  filtering option used the absolute number of recovered reads instead.
* Added PctRecovery to the tables in Samplevis HTML visualisations.
* BGPredict will now print a nice error message if the -n/--min-pct
  option is set to zero or a negative number, to avoid division by zero.
* Samplestats would crash if the input file contained the flags column.
* FDSTools would crash when trying to convert sequences to allele names
  using a TSSV library.

Improved:
* Libconvert will no longer include duplicate sequences in the STR
  defenition when converting to TSSV format and the reference sequence
  of one of the markers is the same as one of its aliases, or when
  aliases of one marker share one or more prefix or suffix sequences.
* Updated add_input_output_args() such that the output file is a
  positional argument (instead of -o) for tools that have a single input
  file and no support for batches.
* Updated add_sequence_format_args() such that the library file can be
  made a required argument.
* Refined the FDSTools package description, since FDSTools does more
  than just noise filteirng.
* FDSTools will now do a marginally better job at producing allele names
  for sequences that do not exactly match the provided STR pattern. When
  seeking the longest matching portion of the sequence, it will now also
  test the reversed sequence with a reversed pattern, which sometimes
  yields a longer match. It is still not optimal, though, but some
  refactoring has been done to move away from regular expressions.
* BGCorrect will now also fill in correction_flags for newly added
  sequences.
* Adjusted the help text of Samplestats to include the fact that the -c
  and -y options have an OR relation instead of an AND relation.
* BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict, and
  Stuttermodel will now ignore special values that may appear in the
  place of a sequence (currently: 'Other sequences' and 'No data').

Removed:
* The -m/--marker-column and -a/--allele-column arguments of BGPredict
  had no effect and have been removed.

Visualisations:
* Updated bundled D3 to v3.5.12.
* In HTML visualisations, if the page is scrolled to the right edge when
  an option is changed that causes the graphs to become wider, the page
  now remains scrolled to the right.
* Samplevis HTML visualisations:
  * Added 'Clear manually added/removed' link to the table filtering.
  * Reduced flicker of the mouse cursor in Internet Explorer.
  * Added 'Common axis range' checkbox (only available when 'Split
    markers' is off).
  * Added 'Save table' link to save the table of selected alleles to a
    tab-separated file.
  * Added 'PctRecovery' column to the tables of selected alleles.
  * An alert box is now shown when a data file is loaded that contains
    markers that have 'No data'.
  * Added 'Percentage of total reads' to the graph filtering options.
  * Added a note to the table filtering options to explain that the
    minimum percentage correction and recovery have an OR relation.

Fixed:
* When converting STR allele names to sequences, FDSTools would reject
  any prefix variants with a false message stating that the variant does
  not match the reference sequence.
* The Samplestats tool would not allow the -b/--min-per-strand option to
  be set to zero.

Improved:
* Moved the flags generated by BGCorrect to a new column named
  correction_flags. Some of the values have been renamed for clarity,
  and this column now always contains a value.
  * The Samplestats tool will no longer add the not_corrected flag to
    each sequence, as it does not add the correction_flags column.
* The Samplestats tool now supports filtering sequences. For filtering,
  the same set of options is available as those used for marking
  alleles. The filtering options use upper case letters and have '-filt'
  appended to their long name. The new -a/--filter-action option defines
  what should be done with filtered sequencies. 'off', the default,
  disables filtering; 'combine' replaces filtered sequences with a new
  line containing aggregated data; 'delete' removes filtered sequences
  without leaving a trace.
  * The seqconvert tool is aware of the special 'Other sequences' value
    produced by Samplestats with -a/--filter-action set to 'combine'.
	Other tools will give an informative error message when the input
	contains this special value.
* The Samplestats tool now accepts non-integer and negative numbers for
  -n/--min-reads and -b/--min-per-strand because after correction read
  counts are not necessarily nonnegative integers anymore.
* The forward_correction and reverse_correction columns of Samplestats
  will now contain 0 if the sequence had exactly 0 reads both before and
  after correction (previously, this was -100).
* Renamed the _mp columns of Samplestats to _mp_sum ("per-marker
  percentage of the sum") and introduced _mp_max columns ("per-marker
  percentage of the maximum").
* Samplestats and Samplevis HTML visualisations will now mark a sequence
  as 'allele' if the minimum amount of correction OR the minimum number
  of recovered reads is reached (as opposed to AND). This allows alleles
  on stutter positions to be detected.

Changed:
* The -r/--min-recovery option of Samplestats has been renamed to
  -y/--min-recovery, analogous to the new -Y/--min-recovery-filt.

Visualisations:
* Updated Vega to version 2.4.1.
* Replaced the regular expression-based filters in all visualisations
  with a much simpler syntax. The new syntax uses space-separated search
  terms, defaulting to a 'contains'-type search method. If any search
  term is preceded by an equals sign, that term must be matched exactly.
  (The search terms themselves are actually still matched as regexes!)
* Added 'show negative alleles' option (default on) to Samplevis. When
  enabled, the graph filtering options work on abs(value) instead of the
  value itself.
* When sorting alleles in Samplevis, the allele name is now used as the
  final tiebreaker instead of the primary sorting column.
* HTML visualisations no longer re-render the entire graph when changing
  the width. The same holds true for the height setting of Allelevis.
* The tables in Samplevis HTML visualisations will now contain the
  information from BGCorrect's correction_flags column in the Notes
  column.

Fixed:
* In Samplevis HTML visualisations, the automatic allele selection was
  only checking the number of reverse reads for the 'minimum number of
  reads per orientation' setting.
* In Samplevis HTML visualisations, automatic allele selection would
  fail to select alleles that had exactly the given minimum number of
  reads.
* FDSTools would sometimes calculate incorrect and even negative repeat
  counts when producing TSSV-style sequences and allele names for
  sequences that did not exactly fit the STR structure given in the
  library.

Improved:
* The Samplestats tool now offers the same possibilities to mark alleles
  as Samplevis HTML visualisations do.
* In Samplevis HTML visualisations, user-removed alleles now have a line
  through their table row.
* Added a reference to https://docs.python.org/howto/regex in the sample
  tag parsing options section of the help text of many tools.
* FDSTools will now do a better job of finding the longest possible
  match of the STR repeat definition to produce TSSV-style sequences and
  allele names for seqences that do not exactly fit the STR structure
  given in the library.

Added:
* New visualisation type 'allele'. With Allelevis, you can generate a
  graph of the alleles of the reference samples (output from
  Allelefinder). (Known bug: it has a 'funny' amount of padding.)

Fixed:
* The Vis tool no longer crashes if you specify '-' as the input file
  without piping data in from another program. It will just produce a
  visualisation file with no embedded data instead.
* FDSTools would crash when generating an allele name for a sequence of
  an STR marker that contained the prefix and suffix of the marker but
  not the actual STR (yes, this happened).
* Stuttermodelvis would draw all 'All data' fits in the graphs of all
  repeat unit sequences, instead of just the 'All data' fit that was
  fitted to the data of a particular repeat sequence.

Improved:
* BGHomStats, BGHomRaw, and Samplestats now round their output to three
  significant digits.
* BGCorrect now rounds its output to 3 decimal positions.

Various enhancements to Samplevis HTML visualisations:
* Added a whole new set of options which are used to automatically
  select the true alleles in a sample.
* Added an option to split the graphs and the table up per marker.
* The selected alleles are no longer lost when the graphs are
  re-rendered due to changed options.
* Added some more columns to the table of selected alleles and made the
  table prettier.
* Added a dedicated stylesheet for printing, which transforms the web
  page into a nicely formatted report when printed.
* Option groups can now be hidden separately.
* Filtering options are now based on the read numbers after correction.
* The mouse cursor now changes to a 'pointer' style cursor (usually a
  hand with stretched index finger) when hovered over the clickable
  portion of the graph.

Visualisations:
* Updated Vega to version 2.4.0 and d3 to version 3.5.10.
* All visualisations now use signals to set the options. This allows
  them to be updated without re-parsing the entire graph spec in most
  cases, which is much faster.
* Using new cross-and-filter capabilities in bgrawvis, profilevis,
  samplevis, and stuttermodelvis. This greatly reduces Vega's memory
  usage and speeds up rendering.
* The name of the currently loaded data file is prepended to the page
  title in HTML visualisations.
* If a file is loaded into an HTML visualisation by drag-and-drop, the
  name of the loaded file is displayed on the file input element.
* A new -T/--title option for the Vis tool allows for specifying
  something that should be prepended to the page title of HTML
  visualisations. This is particularly useful when data is piped in,
  because no file name is available in that case.
* Asynchronous rendering of visualisations is now cancelled if a new
  asynchronous rendering task has already been scheduled (HTML
  visualisations only).

* New tool Samplestats computes various sequence-centric statistics for
  sample data files. Most statistics relate to correction amounts and
  are thus only included if the input file contains BGCorrect columns.
* The starting position can now be ommitted from the [genome_position]
  in FDSTools library files. A default value of 1 will be used in this
  case.
* The setup.py script can now also be run without explicitly specifying
  Python as the interpreter (it now has a shebang line).

Fixed:
* The 'to' base in variants called on mtDNA was incorrect. This bug could also cause FDSTools to crash.
* FDSTools would crash if you tried to generate an allele name for a primer dimer of an mtDNA marker. (Now, you get an insane but entirely accurate allele name instead.)
* Fixed bug that caused some perfectly valid mtDNA allele names to be rejected when attempting to convert them back to raw sequences.

Improved:
* You can now also specify the ending position of the markers in the FDSTools library. If you do, you may also additionally specify a second start position (and optionally also a second end position, and so on). FDSTools will interpret this as that the marker is the concatenation of each of these fragments. This was primarily introduced to support mtDNA fragments that contain (somewhere in the middle) the origin of mtDNA base numbering.
* More helpful error message when format violations are detected while parsing the library file.
* More helpful error message when the -e/--tag-expr regular expression could not be compiled.
* Added a paragraph about sequence alignment caching to the help text of Seqconvert.
* Added a 'flags' column to BGCorrect output, which gives information about the data that was used to do the correction.

Background noise profiles:
* Removed -C/--cross-tabular option from BGEstimate, BGPredict, and BGMerge and also removed the ability to read files in this format.
* BGEstimate, BGHomStats, and BGPredict now add a column 'tool' with their name to the output.

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.

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 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 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.

* 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.

* New tool StutterModel fits polynomials to stutter ratio vs repeat
  length.
* Changed -R to -Q (--limit-reads) so that I can reassign -R to an
  option that is used more often.
* Changed -r to -R (--report) to make sure it will not collide with
  the -r option in Stuttermark, if I ever want to add report output
  to Stuttermark.
* BGHomStats now checks whether all alleles are detected

* 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).

* New tool BGHomStats computes statistics (minimum, maximum, mean,
  and sample variance) of noise ratios in homozygous samples.
* The default BGEstimate output format has been changed to be
  compatible with that of BGHomStats. The cross-tabular output
  format is still available as an option because it easily uses 90%
  less disk space. BGCorrect (and other future tools that use noise
  profiles) will work with both formats.
* Fixed bug in the --min-samples option of BGEstimate that could
  cause some alleles with less than the specified number of samples
  to be included if --drop-samples is used at the same time.
* The user now receives an error message if there are unknown
  arguments. The error message lists the usage string of the
  requested tool. (Argparse's default was to print the general
  FDSTools usage string, which is not helpful.)

* Unknown arguments are now silently ignored. If this results in
  the tool not being able to run, the usage information of the tool
  is printed instead of the general fdstools usage.
* Seqconvert no longer crashes on an empty line in the input.
* Libconvert now maintains the order of prefix/suffix sequences.
* Allele names with aliases other than 'X' or 'Y' are now correctly
  recognised. These were previously rejected as 'unknown format'.
* Fixed bug where a prefix/suffix other than the first listed in
  the library file was sometimes used as the canonical sequence.
* Sequence format conversion from raw to TSSV-style sequences now
  attempts to match the prefix, suffix, and STR pattern to
  non-matching sequences on a best effort basis. This is
  especially useful when converting to allelenames (which is done
  via TSSV-style sequences), since it results in an allele name
  that matches more closely the names of other alleles.
* Generating allele names for sequences that lack a prefix and/or
  suffix is now supported (by adding a variant description that
  deletes the entire prefix/suffix).

* 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.

I could write about all its features here, but instead I will point
out some future plans to highlight the things that are possibly not
optimal in their current implementation.

There are a number of things I plan to change in the future:
* The output format is currently JSON, perhaps a carefully designed
  tabular format is a better choice. The benefit of switching to a
  tabluar format is that the data can be loaded into e.g. Excel as
  well.
* The profiles are currently produced separately for forward and
  reverse reads. I would prefer to integrate these into a single
  computation that estimates allele balance in the heterozygotes
  using both strands as well.
* I would like to add information about strand bias of the alleles
  as well. The most straightforward way to do this is to set only
  the forward reads of the true allele to 100 and treat the reverse
  reads the same as all background products. You will then obtain a
  number of reverse reads observed for ever 100 forward reads of
  the true allele.
* I think it would be appropriate to make sure the values in the
  allele balance matrices of each sample ('Ax' in the source code)
  should add up to 1. For homozygotes, it is currently a scalar 1,
  the sum of the elements tend to be more than 1. This means that a
  heterozygous sample has a stronger influence on the profiles than
  a homozygous sample.

* Allelefinder can now combine data from multiple files into a
  single sample (this happens when the same sample tag was
  extracted from their names).
* Allelefinder can now automatically convert sequences to a given
  format (this is optional though). This is particularly useful
  when combining the knownalleles.csv and newalleles.csv files of
  a sample. (Note that allelefinder still assumes that the files
  contain different alleles; no attempt is made to check whether
  the same allele was represented in multiple files.)

* Fixed crash when attempting to read a TSSV library from sys.stdin.
* Various large updates to allelefinder.
* libconvert now gives a useful default FDSTools library when given
  no input.

* Introducing a new, extended library file format to support
  allele name generation.  The new libconvert tool can convert
  TSSV libraries to the new format and vice versa.
* Added functions for converting between raw sequences, TSSV-style
  sequences, and allele names.
* Added global -d/--debug option.

Stuttermark updates:
* Stuttermark now automatically converts input sequences to
  TSSV-style if a library is provided.
* Stuttermark will no longer crash if there is no 'name' column.
  Instead, all sequences are taken to belong to the same marker.

New tools:
* libconvert converts between FDSTools and TSSV library formats.
* seqconvert converts between raw sequences, TSSV-style sequences,
  and allele names.
* allelefinder detects the true alleles in reference samples.

FDSTools v0.0.1 with Stuttermark v1.3.
Other tools will come later.