• 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.
      * Added new tool BGAnalyse which can be used to analyse the remaining amount
        of noise in reference samples after correction.  This tool is a more
        sensitive successor of the 'Blame' tool.
      * Added new visualisation BGAnalysevis for visualising data obtained from
        BGAnalyse. This visualisation allows for identifying unclean or otherwise
        suboptimal samples by comparing the lowest, highest, and/or total remaining
        noise after correction for each marker in each sample.
      * The Blame tool was removed in favour of BGAnalyse.
    * Libconvert v1.1.0:
      * When converting to FDSTools format, Libconvert automatically creates an
        empty FDSTools library file with the same contents as what would be
        obtained from the new Library tool without arguments.
      * The -a/--aliases option was modified such that it has the same effect as
        the -a/--aliases option of the new Library tool. This means that without
        this option specified, the [aliases] section will not be present in the
        output anymore.
      * The ability of the Libconvert tool to produce an empty FDSTools library
        file if no input file was given has been removed from the documentation
        (but not from the tool itself).
    * TSSV v1.0.2:
      * Added new option -n/--indel-score which can be used to increase the
        penalty given to insertions and deletions in the flanking sequences w.r.t.
        the penalty given to mismatches.
      * NOTE: Requires TSSV v0.4.0 or newer to be installed.
    * Vis v1.0.2:
      * Changed default value of -n/--min-abs from 15 to 5.
      * Added -I/--input2 option, which allows for specifying a file with raw data
        points for Stuttermodelvis and Profilevis.
      * Added support for creating BGAnalysevis visualisations.
    * Profilevis v2.0.0:
      * Replaced the simple Options overlay with responsive design options panels
        in HTML visualisations.
      * Alleles and sequences are now sorted by CE allele length when applicable.
      * Added option to plot BGHomRaw data on top of the profiles.
      * Added marker selection menu for easier filtering.
    * BGRawvis v2.0.0:
      * Replaced the simple Options overlay with responsive design options panels
        in HTML visualisations.
      * Sequences are now sorted by CE allele length when applicable.
      * Changed default minimum number of reads from 15 to 5.
      * Added marker selection menu for easier filtering.
    * Stuttermodelvis v2.0.0:
      * Replaced the simple Options overlay with responsive design options panels
        in HTML visualisations.
      * Fixed glitch that caused the graphs to be re-rendered twice when loading
        a file by drag-and-drop in HTML visualisations.
      * Fixed glitch that made it possible to replace the data that was embedded
        in an HTML visualisation through drag-and-drop.
      * Added repeat unit selection menu for easier filtering.
    * Allelevis v2.0.0:
      * Replaced the simple Options overlay with responsive design options panels
        in HTML visualisations.
      * Reduced Vega graph spec complexity by using the new Rank transform to
        position the subgraphs.
      * Fixed glitch that caused unnecessary padding around the graph.
    * Samplestats v1.1.0:
      * Changed default allele calling option thresholds:
        * Changed default value of -m/--min-pct-of-max from 5.0 to 2.0.
        * Changed default value of -p/--min-pct-of-sum from 3.0 to 1.5.
      * Mentioned allele calling in the tool descriptions.
    * Samplevis v2.1.0:
      * Changed default minimum number of reads for graph filtering from 15 to 5.
      * Changed default table filtering options:
        * Percentage of highest allele per marker changed from 5% to 2%.
        * Percentage of the marker's total reads changed from 3% to 1.5%.
        * Minimum number of reads in both orientations changed from 0 to 1.
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