• 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