1. 19 Mar, 2019 1 commit
    • Hoogenboom, Jerry's avatar
      TSSV v2.0.0 · bf7a9aff
      Hoogenboom, Jerry authored
        - Removed dependency on external tssv package (it is no longer compatible).
        - Greatly increased performance by deduplicating the input reads.
        - Removed the -q/--is-fastq option in favour of automatic detection.
        - Changed the default value for -m/--mismatches from 0.08 to 0.1.
        - Changed the default value for -n/--indel-score from 1 to 2.
        - Added the -X/--no-deduplicate option to disable deduplication.
        - Fixed potential crash that could occur under very specific circumstances.
  2. 07 Dec, 2018 1 commit
  3. 03 Jul, 2018 1 commit
  4. 15 Mar, 2017 1 commit
  5. 14 Mar, 2017 1 commit
  6. 21 Dec, 2016 1 commit
  7. 03 Oct, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.0.0 Release Candidate 1 · de3593a8
      Hoogenboom, Jerry authored
      * 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 t...
  8. 06 Sep, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v0.0.5: new tools, changed defaults · abba1c04
      Hoogenboom, Jerry authored
      * 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...
  9. 27 Jul, 2016 1 commit
  10. 08 Mar, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Version numbering for everything · da8d1d1b
      Hoogenboom, Jerry authored
      * Turned all '0.1dev' tool version numbers to '1.0.0'.
      * Changed Stuttermark's version number from '1.5' to '1.5.0'.
      * Added version numbers to the visualisations.
      * Updated README.rst to include all tools, but removed the usage details
        of Stuttermark because it is highly impractical to include usage
        details for all tools in the README file. I'll leave that to the
        -h/--help option and the yet-to-write FDSTools User's Handbook.
  11. 04 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Fix crash in Samplevis HTML visualisations · 2d1fffde
      Hoogenboom, Jerry authored
      * Fixed a javascript crash in Samplevis HTML Visualisations.
      * Converted two unexpected tab characters to spaces in README.rst.
      * Samplestats will now sort the output by marker name.
  12. 02 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Big update: Bumped version to v0.0.3 · ebf700a7
      Hoogenboom, Jerry authored
      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.
      * 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.
      * 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.
      * 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
      * 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').
      * The -m/--marker-column and -a/--allele-column arguments of BGPredict
        had no effect and have been removed.
      * 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.
  13. 24 Jul, 2015 1 commit
  14. 23 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Laying foundations · 160594c5
      jhoogenboom authored
      * 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.
  15. 02 Jul, 2015 2 commits