1. 25 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Introducing findnewalleles · 4148bb50
      Hoogenboom, Jerry authored
      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.
      4148bb50
  2. 09 Dec, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Filtering and aggregation in Samplestats · a3e610e8
      Hoogenboom, Jerry authored
      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.
      a3e610e8
  3. 01 Dec, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Grand update to all visualisations, especially Samplevis · e7517bbd
      Hoogenboom, Jerry authored
      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).
      e7517bbd
  4. 01 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Various bug fixes and additions · ce7f34fb
      jhoogenboom authored
      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.
      ce7f34fb
  5. 26 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGRawVis · 8213ec14
      jhoogenboom authored
      * Added new visualisation BGRawVis to the Vis tool. It visualises BGHomRaw output data.
      * Now using more reliable linear X axis label formatting in Profilevis.
      * Changed filtering operands in Profilevis and Samplevis from > to >=.
      8213ec14
  6. 24 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Added Profilevis to the Vis tool and added various enhancements. · 513f967a
      jhoogenboom authored
      * 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.
      513f967a
  7. 21 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Profilevis, and various bug fixes · b7d64a4f
      jhoogenboom authored
      * 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.
      b7d64a4f