• 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
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