GitLab

* Samplevis now features a responsive design. The options have been
  moved from the overlay into a menu bar that changes place and shape
  depending on the width and height of the viewport.
* All option labels are now clickable. When clicked, the corresponding
  option receives focus.
* The 'Save image', 'Save table', and 'Clear manually added/removed'
  links are now always visible, but change appearance when unavailable.
* When a 'No data' line is found for one or more markers, a warning is
  displayed at the bottom of the screen.
* Fixed bug that caused user-selected and user-removed alleles to get
  lost when the corresponding marker is filtered out using the marker
  name filter.
* Fixed bug in the printing stylesheet that caused conforming browsers
  to break pages between the graph and the table of a marker, instead of
  avoiding to do so.
* In HTML visualisations with embedded data, the name of the sample data
  file is now shown in the place of the file selection element.

Other Samplevis fixes and improvements:
* Added option to show sequences that are filtered from the graphs as a
  single 'Other sequences' aggregate entry per marker (default: on).
* For alleles that end up at a negative read count after correction now
  have a strand balance line in the 'overlap' portion of their bar only.
* The strand bias mark is now correctly positioned when using the square
  root scale.

Improved:
* HTML visualisations with embedded data will now use a proper filename
  for the 'Save graph' and 'Save table' options.

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:
* Fixed a crash in BGMerge.
* Fixed bug in BGCorrect that resulted in incorrect values in the
  *_add and *_corrected columns (yes, you, 8685a304).
* Fixed a glitch in BGCorrect that prevented it from ever writing
  corrected_bgestimate in the correction_flags column.

Improved:
* BGEstimate will now include the sample tag in the error messages for
  missing alleles and alleles with 0 reads.
* Strand bias lines in Samplevis are now clamped to the 0-100% range.
  BGCorrect may cause forward read percentages outside this range.

Visualisations:
* Updated Vega to version 2.4.2.
* Fixed drag-'n-drop behaviour for HTML visualisations in Internet
  Explorer and Firefox.
* Fixed the Save Image link when viewing HTML visualisations in
  Internet Explorer 10 and above.
* Added http-equiv="X-UA-Compatible" content="IE=edge" meta-tag to all
  visualisations to prevent Internet Explorer from entering quirks mode.
* Samplevis:
  * Fixed glitch that would sometimes cause a second horizontal scroll
    bar to appear.
  * Graphs now render much more quickly when 'Split markers' is on, and
    Chrome no longer crashes on large sample files with this option set.

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.

* 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.