1. 26 Jul, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Various bug fixes and refinements throughout FDSTools · 08cf6ddd
      Hoogenboom, Jerry authored
      * 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.
      08cf6ddd
  2. 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
  3. 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
  4. 29 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Introducing bgestimate · be745e64
      jhoogenboom authored
      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.
      be745e64
  5. 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.
      160594c5
  6. 02 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Initial commit · 668970ed
      jhoogenboom authored
      FDSTools v0.0.1 with Stuttermark v1.3.
      Other tools will come later.
      668970ed