1. 01 Apr, 2019 1 commit
  2. 29 Mar, 2019 1 commit
  3. 22 Mar, 2019 1 commit
  4. 19 Mar, 2019 2 commits
    • Hoogenboom, Jerry's avatar
      Samplestats v1.2.0 · 1e0e3792
      Hoogenboom, Jerry authored
        - Fixed bug where the 'Other sequences' could be treated as the maximum
          against which the '*_mp_max' columns are calculated.
      1e0e3792
    • Hoogenboom, Jerry's avatar
      TSSV v2.0.0 · bf7a9aff
      Hoogenboom, Jerry authored
        - Removed dependency on external tssv package (it is no longer compatible).
        - Greatly increased performance by deduplicating the input reads.
        - Removed the -q/--is-fastq option in favour of automatic detection.
        - Changed the default value for -m/--mismatches from 0.08 to 0.1.
        - Changed the default value for -n/--indel-score from 1 to 2.
        - Added the -X/--no-deduplicate option to disable deduplication.
        - Fixed potential crash that could occur under very specific circumstances.
      bf7a9aff
  5. 07 Dec, 2018 1 commit
  6. 03 Jul, 2018 1 commit
  7. 15 Mar, 2017 1 commit
  8. 14 Mar, 2017 1 commit
  9. 08 Mar, 2017 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.1.0.dev3: Fixes and pipelining enhancements · be8dbe46
      Hoogenboom, Jerry authored
      * General changes in v1.1.0.dev3:
        * Allele name heuristics: don't produce insertions at the end of the
          prefix or at the beginning of the suffix; just include extra STR
          blocks.
        * FDSTools will no longer crash with a 'column not found' error when
          an input file is empty. This situation is now treated as if the
          expected columns existed, but no lines of actual data were present.
          This greatly helps in tracking down issues in pipelines involving
          multiple tools, as tools will now shutdown gracefully if an upstream
          tool fails to write output.
      * Allelefinder v1.0.1:
        * Fixed crash that occurred when converting sequences to allele names
          format while no library file was provided.
        * Don't crash when output pipe is closed.
      * BGAnalyse v1.0.1:
        * Don't crash when output pipe is closed.
      * BGCorrect v1.0.2:
        * Don't crash on empty input files.
        * Don't crash when output pipe is closed.
      * BGEstimate v1.1.2:
        * Don't crash when output pipe is closed.
      * BGHomRaw v1.0.1:
        * Clarified the 'Allele x of marker y has 0 reads' error message with
          the sample tag.
        * Don't crash when output pipe is closed.
      * BGHomStats v1.0.1:
        * Error messages about the input data now contain the sample tag of
          the sample that triggered the error.
        * Don't crash when output pipe is closed.
      * BGMerge v1.0.3:
        * Don't crash when output pipe is closed.
      * BGPredict v1.0.2:
        * Don't crash on empty input files.
        * Don't crash when output pipe is closed.
      * FindNewAlleles v1.0.1:
        * Don't crash on empty input files.
        * Don't crash when output pipe is closed.
      * Libconvert v1.1.2:
        * Don't crash when output pipe is closed.
      * Library v1.0.3:
        * Don't crash when output pipe is closed.
      * Seqconvert v1.0.2:
        * Don't crash when output pipe is closed.
      * Samplestats v1.1.1:
        * Don't crash on empty input files.
        * Don't crash when output pipe is closed.
      * Stuttermark v1.5.1:
        * Don't crash on empty input files.
        * Don't crash when output pipe is closed.
      * Stuttermodel v1.1.2:
        * Don't crash when output pipe is closed.
      * TSSV v1.1.0 (additionally):
        * When running analysis in parallel, make tasks of 1 million alignments.
          Previously, this was 10k reads, with the number of alignments per task
          depending on the size of the library file. This caused memory issues for
          huge libraries like whole mt interval libraries.
        * Don't crash when output pipe is closed.
      * Vis v1.0.4:
        * Don't crash when output pipe is closed.
      be8dbe46
  10. 09 Feb, 2017 1 commit
  11. 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
  12. 21 Dec, 2016 2 commits
    • Hoogenboom, Jerry's avatar
      Release v1.0.1 · bbb08573
      Hoogenboom, Jerry authored
      bbb08573
    • Hoogenboom, Jerry's avatar
      FDSTools v1.0.1.dev3 · 14b17206
      Hoogenboom, Jerry authored
      * General changes in v1.0.1:
        * Fixed crash that occurred when using the -i option to run the same command
          on multiple input files.
        * The usage string now always starts with 'fdstools', even if FDSTools was
          invoked using some other command (e.g. on Windows, FDSTools gets invoked
          through a file called 'fdstools-script.py').
        * Fixed bug with the -d/--debug option being ignored if placed before the
          tool name on systems running Python 2.7.9 or later.
        * FDSTools library files may now contain IUPAC ambiguous bases in the
          prefix and suffix sequences of STR markers (except the first sequence,
          as it is used as the reference).  Additionally, optional bases may be
          represented by lowercase letters.
        * If no explicit prefix/suffix is given for an alias, the prefix/suffix of
          the corresponding marker is assumed instead. This situation was not
          handled correctly when converting from raw sequences to TSSV or allelename
          format, which resulted in the alias remaining unused.
      * Stuttermodelvis v2.0.2:
        * Added filtering option for the stutter amount (-1, +1, -2, etc.).
        * Added filtering option for the coefficient of determination (r squared
          value) of the fit functions.
      * Libconvert v1.1.1:
        * Adjustments for supporting IUPAC notation in prefix and suffix sequences
          when converting from FDSTools to TSSV library format.
      * Library v1.0.2:
        * Added documentation for IUPAC support to the descriptive comment of the
          [prefix] section.
      14b17206
  13. 26 Oct, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      FDSTools v1.0.1.dev2 · 98c434ed
      Hoogenboom, Jerry authored
      * Samplevis v2.1.2 (additionally):
        * The net effect of the allele calling thresholds (table filtering options)
          is now visualised in the graphs as a dashed vertical red line.
        * Fixed issue with allele calling thresholds not working anymore after having
          used the 'Save page' link in HTML visualisations.
      98c434ed
  14. 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
  15. 03 Oct, 2016 4 commits
    • Hoogenboom, Jerry's avatar
    • Hoogenboom, Jerry's avatar
    • Hoogenboom, Jerry's avatar
      Changing Development Status from Alpha to Beta · 70af0449
      Hoogenboom, Jerry authored
      There is no 'Release Candidate' classifier, so this is the next best thing.
      70af0449
    • 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 tables in HTML visualisations will now grow much wider than
          before if the screen (or window) is very narrow.
        * In the tables 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.
        * Improved determination of column widths of the allele tables when printing
          an HTML visualisation.
        * When printing an HTML visualisation, the graph and the corresponding table
          of a marker will be kept on the same page in all browsers now.
        * Fixed glitch that caused 'Infinity%' or 'NaN%' to be written in some cells
          in the allele tables in HTML visualisations for sequences that had zero
          reads (before or after correction).  These cells will remain empty now.
      * Pipeline v1.0.1 (additionally):
        * The Pipeline tool will now only write the command lines of the tools it
          runs if the -d/--debug option was specified.
      * Library v1.0.1 (additionally):
        * Added proper examples for non-STR markers and aliases.
      * Stuttermodel v1.1.1:
        * Minor change to internal variant representation.
      de3593a8
  16. 20 Sep, 2016 2 commits
    • Hoogenboom, Jerry's avatar
      Update version number to v0.0.6.dev1 · 70a3ea3b
      Hoogenboom, Jerry authored
      70a3ea3b
    • 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
  17. 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
  18. 27 Jul, 2016 1 commit
  19. 26 Jul, 2016 1 commit
    • 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
  20. 22 Mar, 2016 2 commits
    • Hoogenboom, Jerry's avatar
      Updates to Samplevis HTML visualisations (mostly the tables) · 3a495653
      Hoogenboom, Jerry authored
      * Added Noise column to the allele tables.
      * Added number of reads before correction to the allele tables.
      * Added raw numbers of reads to the Correction and Recovery columns of
        the allele tables.
      * Fixed issue with Samplevis HTML visualisations in Firefox and Internet
        Explorer that caused an uncessesary horizontal scroll bar in the
        options panel.
      3a495653
    • Hoogenboom, Jerry's avatar
      PctRecovery relative to number of reads after correction · 0065d2cb
      Hoogenboom, Jerry authored
      Changed:
      * The PctRecovery as used for automatic allele selection in Samplevis
        HTML visualisations as well as Samplestats is now computed w.r.t. the
        number of reads after correction, instead of the number of reads
        before correction.
      
      Added:
      * Added X_recovery columns to the output of the Samplestats tool. The
        value is equal to X_add / X_corrected * 100.
      0065d2cb
  21. 21 Mar, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Fixed Samplevis allele selection glitch, removed TSSV -L · 9565c837
      Hoogenboom, Jerry authored
      Fixed:
      * Fixed a glitch in Samplevis HTML visualisations, where it would fail
        to correctly maintain the user-(de)selected alleles when switching
        Split Markers on or off.
      
      Removed:
      * Removed -L/--check-length option from the TSSV tool, because it had no
        effect. Instead, the TSSV tool will always enforce the expected allele
        lengths specified in the library file. Behaviour has not changed.
      9565c837
  22. 14 Mar, 2016 1 commit
  23. 10 Mar, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Allelefinder fixes and mtDNA allele naming · e30c0408
      Hoogenboom, Jerry authored
      Fixed:
      * The -c/--stuttermark-column option of Allelefinder was not filtering
        out the non-ALLELE sequences as it was supposed to. (This issue was
        introduced in ce7f34fb, in which a bug was fixed that caused this
        option to filter all sequences, including the ones marked with ALLELE.
        So it turns out this option has been broken since 732e83ba.)
      
      Improved:
      * Allelefinder will no longer reject a marker based on the number of
        reads of 'Other sequences'.
      * Adjusted sequence alignment parameters for mtDNA sequences to produce
        allele names that more closely follow historical mtDNA mutation
        nomenclature.
      e30c0408
  24. 09 Mar, 2016 1 commit
  25. 08 Mar, 2016 2 commits
    • Hoogenboom, Jerry's avatar
      Version numbering for everything · da8d1d1b
      Hoogenboom, Jerry authored
      * Turned all '0.1dev' tool version numbers to '1.0.0'.
      * Changed Stuttermark's version number from '1.5' to '1.5.0'.
      * Added version numbers to the visualisations.
      * Updated README.rst to include all tools, but removed the usage details
        of Stuttermark because it is highly impractical to include usage
        details for all tools in the README file. I'll leave that to the
        -h/--help option and the yet-to-write FDSTools User's Handbook.
      da8d1d1b
    • Hoogenboom, Jerry's avatar
      Improved sequence aligment (variant calling) quality · e1bd3e41
      Hoogenboom, Jerry authored
      FDSTools would sometimes produce suboptimal alignments. Most notably, it
      it would produce multiple smaller insertions/deletions when the
      difference between two sequences could be described by one larger
      insertion/deletion in combination with a base substitution. The latter
      description is often more biologically sound and also usually results in
      a shorter allele name.
      
      * Fixed a bug that sometimes caused FDSTools to choose an incorrect path
        through the alignment matrix, producing a suboptimal alignment.
      * Tweaked the alignment parameters to produce more meaningful results.
      e1bd3e41
  26. 07 Mar, 2016 1 commit
  27. 01 Mar, 2016 1 commit
  28. 29 Feb, 2016 3 commits
    • Hoogenboom, Jerry's avatar
      PROPER FIX THIS TIME · 03bfeed9
      Hoogenboom, Jerry authored
      03bfeed9
    • Hoogenboom, Jerry's avatar
      1d17b02d
    • Hoogenboom, Jerry's avatar
      Expected allele lengths, and more · 29fcc171
      Hoogenboom, Jerry authored
      Added:
      * Added a new section expected_allele_length to the FDSTools library
        format. In this section, the minimum and (optionally) maximum allele
        length of each marker can be specified.
      * Added -L/--check-length option to the TSSV tool. If specified, the
        tool will use the expected_allele_length values to filter the results.
      * Samplevis can now truncate long allele names to a given number of
        characters (defaulting to 70).
      * Added an option to Samplestats to keep negatives when filtering (abs
        filter).
      
      Changed:
      * Renamed the --aggregate-below-minimum option of the TSSV tool to
        --aggregate-filtered.
      
      Improved:
      * Added an option to read_sample_data_file such that other code can
        request or require that the X_corrected columns are used.
      * Samplestats will now round to 4 or 5 significant digits if a value is
        above 1000 or 10000, respectively.
      * BGHomRaw will no longer round the forward, reverse, and total columns.
      * When generating mtDNA allele names, FDSTools will now try to avoid
        creating gaps in the alignment of the sequences against the reference.
      * Grouped the filtering options of the TSSV tool in its help text.
      * Cleaned up some leftover code for special sequence value handling
        (more specifically: code that expected ensure_sequence_format to
        return False for special sequence values, which it no longer does).
      * Cleaned up some dead legacy code in reduce_read_counts.
      29fcc171
  29. 25 Feb, 2016 1 commit
    • 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
  30. 22 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Fixed a crash in Samplestats, and minor improvements · 13e0d781
      Hoogenboom, Jerry authored
      Fixed:
      * Fixed crash in Samplestats. It would crash if BGCorrect columns were
        present.
      * Fixed glitch in Samplevis that allowed clicking the 'Other sequences'
        bars if the input data already contained the 'Other sequences' entry.
      
      Improved:
      * The TSSV tool will now drop any sequences that contain anything other
        than A, C, T, and G. If the -A option is given, these sequences will
        still be added to the marker aggregates. Many other tools will fail
        when confronted with such invalid sequences, especially when allele
        names need to be generated.
      * In Samplevis, the sequences are now consistently sorted (except for
        some inconsistency caused by a bug in Vega). The sorting is based on
        read counts and is the same as used for the allele tables in Samplevis
        HTML visualisations.
      * Added a comment line that mentions genome build GRCh38 and rCRS to the
        genome_position block in the libconvert output. This is mainly for
        documentation purposes; users are free to change this line if they use
        a different reference.
      * Minor styling changes to Samplevis HTML visualisations.
      13e0d781