1. 29 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Expected allele lengths, and more · 29fcc171
      Hoogenboom, Jerry authored
      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.
      29fcc171
  2. 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
  3. 04 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Updated handling of 'No data' and 'Other sequences' · 9ed2f3d1
      Hoogenboom, Jerry authored
      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.
      9ed2f3d1
  4. 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.
      
      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.
      ebf700a7
  5. 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
  6. 04 Nov, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Implemented support for non-STR markers, improved file handling and more · 1083919c
      Hoogenboom, Jerry authored
      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.
      1083919c
  7. 01 Sep, 2015 2 commits
    • jhoogenboom's avatar
      Cleanup and minor enhancements · 03fc3d49
      jhoogenboom authored
      * 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.
      03fc3d49
    • 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
  8. 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
  9. 25 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGHomRaw. · 20337ba3
      jhoogenboom authored
      * New tool BGHomRaw computes noise ratios for all detected noise in
        all homozygous reference samples. The idea is to plot this data
        in a visualisation that will be added later.
      20337ba3
  10. 10 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Intoducing StutterModel · 818ddd2b
      jhoogenboom authored
      * 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
      818ddd2b
  11. 07 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Reworked input/output file arguments · 7f23c2e0
      jhoogenboom authored
      * 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.
      7f23c2e0
  12. 06 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Greatly increased argument help · b30bdbbc
      jhoogenboom authored
      * 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.
      b30bdbbc
  13. 05 Aug, 2015 1 commit
  14. 04 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Blame · 8685a304
      jhoogenboom authored
      * 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).
      8685a304
  15. 03 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGHomStats · a09131d9
      jhoogenboom authored
      * 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.)
      a09131d9