1. 03 Dec, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Bug fixes and improvements in allele name gen and auto allele selection · 7820cad0
      Hoogenboom, Jerry authored
      Fixed:
      * In Samplevis HTML visualisations, the automatic allele selection was
        only checking the number of reverse reads for the 'minimum number of
        reads per orientation' setting.
      * In Samplevis HTML visualisations, automatic allele selection would
        fail to select alleles that had exactly the given minimum number of
        reads.
      * FDSTools would sometimes calculate incorrect and even negative repeat
        counts when producing TSSV-style sequences and allele names for
        sequences that did not exactly fit the STR structure given in the
        library.
      
      Improved:
      * The Samplestats tool now offers the same possibilities to mark alleles
        as Samplevis HTML visualisations do.
      * In Samplevis HTML visualisations, user-removed alleles now have a line
        through their table row.
      * Added a reference to https://docs.python.org/howto/regex in the sample
        tag parsing options section of the help text of many tools.
      * FDSTools will now do a better job of finding the longest possible
        match of the STR repeat definition to produce TSSV-style sequences and
        allele names for seqences that do not exactly fit the STR structure
        given in the library.
      
      Added:
      * New visualisation type 'allele'. With Allelevis, you can generate a
        graph of the alleles of the reference samples (output from
        Allelefinder). (Known bug: it has a 'funny' amount of padding.)
      7820cad0
  2. 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
  3. 23 Nov, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Introducing Samplestats · 559ee083
      Hoogenboom, Jerry authored
      * New tool Samplestats computes various sequence-centric statistics for
        sample data files. Most statistics relate to correction amounts and
        are thus only included if the input file contains BGCorrect columns.
      * The starting position can now be ommitted from the [genome_position]
        in FDSTools library files. A default value of 1 will be used in this
        case.
      * The setup.py script can now also be run without explicitly specifying
        Python as the interpreter (it now has a shebang line).
      559ee083