1. 07 Feb, 2017 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.1.0.dev1: Visualisation fixes · 4a23b60f
      Hoogenboom, Jerry authored
      * Samplevis v2.2.0:
        * Fixed incorrect calculation of 'percentage of highest' if the 'sequence'
          with the highest read count within a marker is the aggregated 'Other
          sequences' data. In exceptional cases, this could have resulted in the
          erroneous omission of an allele in the visualisation (graphs and/or
          tables).
      * Stuttermodelvis v2.0.3:
        * Fixed bug that caused HTML visualisations with embedded data to fail
          while loading.
        * Fixed glitch where, in HTML visualisations with embedded data and a custom
          title, the custom title was truncated to the last '.' as if it were a file
          name.
      * Pipeline v1.0.3:
        * Fixed glitch that caused the 'bgprofiles.html' output file of the
          reference-database analysis to lack a proper title.
      * BGRawVis v2.0.1:
        * Fixed glitch where, in HTML visualisations with embedded data and a custom
          title, the custom title was truncated to the last '.' as if it were a file
          name.
        * Changed default save filename in HTML visualisations to 'bgprofiles-raw'.
      * Profilevis v2.0.1:
        * Fixed glitch where, in HTML visualisations with embedded data and a custom
          title, the custom title was truncated to the last '.' as if it were a file
          name.
        * Changed default save filename in HTML visualisations to 'bgprofiles'.
      4a23b60f
  2. 13 Oct, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.0.1.dev1 · f2ccd67d
      Hoogenboom, Jerry authored
      * Samplevis v2.1.2:
        * Added 'Save page' link to HTML visualisations, which offers for download a
          copy of the entire HTML visualisation including the user's changes.
        * Added automatic allele calling to static visualisations.
      * Pipeline v1.0.2:
        * Added -A/--in-allelelist option to the pipeline tool to provide an existing
          allele list file when running the ref-db analysis, bypassing Allelefinder.
      * Vis v1.0.3:
        * The -n/--min-abs and -s/--min-per-strand options now accept non-integer
          values as well.
        * Added six options to control the Table Filtering Options of Samplevis.
        * The Display Options now have a separate option group on the command line.
      f2ccd67d
  3. 03 Oct, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.0.0 Release Candidate 1 · de3593a8
      Hoogenboom, Jerry authored
      * General changes in v1.0.0rc1:
        * Fixed bug that caused variant descriptions in allele names of
          non-STR markers to be prepended with plus signs similar to suffix variants
          in STR markers.  When attempting to convert these allele names back to raw
          sequences, FDSTools would crash with an 'Invalid allele name' error.
      * Allelevis v2.0.1 (additionally):
        * In the tooltip in HTML visualisations, a line break may now only be
          inserted in allele names after an underscore character (_) or after a
          repeat block in STR allele names.  If the input file contains raw
          sequences, line breaks may now be introduced anywhere in the sequence.
      * Samplevis v2.1.1:
        * Added tooltip support to HTML visualisations.  Moving the mouse pointer
          over one of the alleles in the graph now displays a tooltip giving
          per-strand read counts of that allele.  The tooltip may include a
          'new allele' note if the input sample was analysed with FindNewAlleles.
        * The allele t...
      de3593a8
  4. 20 Sep, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Developing towards v0.0.6 (v0.0.6.dev1) · 5a2addb7
      Hoogenboom, Jerry authored
      * General changes in v0.0.6.dev1:
        * Tools that take a list of files as their argument (through the -i option or
          as positionals) now explicitly support glob patterns.  This means they will
          interpret '*' and '?' characters as wildcards for 'zero or more characters'
          and 'any one character', respectively.  On Unix-like systems this is
          generally done by the shell, but on Windows one had to specify every file
          name completely.
      * BGEstimate v1.1.1:
        * Added option -p/--profiles which can be used to provide a previously
          created background noise profiles file.  BGEstimate will read starting
          values from this file instead of assuming zero noise.
      * BGMerge v1.0.2:
        * Small code changes to facilitate explicit glob pattern matching support.
      * Pipeline v1.0.1:
        * The Pipeline tool will no longer check the existence of the files specified
          for the -S/--in-samples option; instead, this is left to the downstream
          tools to find out, consistent with how this works with the other input file
          options.
      * Allelevis v2.0.1:
        * Added tooltip support to HTML visualisations.  Moving the mouse pointer
          over a node or edge in the graph now displays a tooltip giving allele names
          and sample counts.
      * Stuttermodelvis v2.0.1:
        * Changed the unit in the horizontal axis title from 'bp' to 'nt'.
      * Library v1.0.1:
        * Updated some of the comments describing the sections.
      5a2addb7
  5. 06 Sep, 2016 1 commit
    • 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.
      abba1c04