1. 08 Mar, 2016 1 commit
    • 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
  2. 29 Feb, 2016 1 commit
    • 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
  3. 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
  4. 02 Feb, 2016 1 commit
    • Hoogenboom, Jerry's avatar
      Big update: Bumped version to v0.0.3 · ebf700a7
      Hoogenboom, Jerry authored
      Updated Stuttermark to v1.5. WARNING: This version of Stuttermark is
      INCOMPATIBLE with output from previous versions of FDSTools and TSSV.
      
      Introducing TSSV-Lite
      * New tool tssv acts as a wrapper around TSSV-Lite (tssvl). Its primary
        purpose is to allow running TSSV-Lite without having to convert the
        FDSTools library to TSSV format, and to offer allelename output. Like
        all other tools in FDSTools, it also works with TSSV library files but
        its allele name generation capabilities are limited in that case.
      
      Changed:
      * TSSV-Lite and the new TSSV tool in FDSTools have two columns renamed
        w.r.t. the original TSSV program: 'name' has been changed to 'marker',
        and 'allele' has been changed to 'sequence'. All tools in FDSTools
        have been updated to use the new column names. This change affects
        Allelefinder, BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict,
        Blame, Samplestats, Samplevis, Stuttermark, Stuttermodel, and
        Seqconvert. Note that this change will BREAK COMPATIBILITY of these
        tools with old data files.
      
      Fixed:
      * In Samplevis HTML visualisations, the "percentage recovery" table
        filtering option used the absolute number of recovered reads instead.
      * Added PctRecovery to the tables in Samplevis HTML visualisations.
      * BGPredict will now print a nice error message if the -n/--min-pct
        option is set to zero or a negative number, to avoid division by zero.
      * Samplestats would crash if the input file contained the flags column.
      * FDSTools would crash when trying to convert sequences to allele names
        using a TSSV library.
      
      Improved:
      * Libconvert will no longer include duplicate sequences in the STR
        defenition when converting to TSSV format and the reference sequence
        of one of the markers is the same as one of its aliases, or when
        aliases of one marker share one or more prefix or suffix sequences.
      * Updated add_input_output_args() such that the output file is a
        positional argument (instead of -o) for tools that have a single input
        file and no support for batches.
      * Updated add_sequence_format_args() such that the library file can be
        made a required argument.
      * Refined the FDSTools package description, since FDSTools does more
        than just noise filteirng.
      * FDSTools will now do a marginally better job at producing allele names
        for sequences that do not exactly match the provided STR pattern. When
        seeking the longest matching portion of the sequence, it will now also
        test the reversed sequence with a reversed pattern, which sometimes
        yields a longer match. It is still not optimal, though, but some
        refactoring has been done to move away from regular expressions.
      * BGCorrect will now also fill in correction_flags for newly added
        sequences.
      * Adjusted the help text of Samplestats to include the fact that the -c
        and -y options have an OR relation instead of an AND relation.
      * BGCorrect, BGEstimate, BGHomRaw, BGHomStats, BGPredict, and
        Stuttermodel will now ignore special values that may appear in the
        place of a sequence (currently: 'Other sequences' and 'No data').
      
      Removed:
      * The -m/--marker-column and -a/--allele-column arguments of BGPredict
        had no effect and have been removed.
      
      Visualisations:
      * Updated bundled D3 to v3.5.12.
      * In HTML visualisations, if the page is scrolled to the right edge when
        an option is changed that causes the graphs to become wider, the page
        now remains scrolled to the right.
      * Samplevis HTML visualisations:
        * Added 'Clear manually added/removed' link to the table filtering.
        * Reduced flicker of the mouse cursor in Internet Explorer.
        * Added 'Common axis range' checkbox (only available when 'Split
          markers' is off).
        * Added 'Save table' link to save the table of selected alleles to a
          tab-separated file.
        * Added 'PctRecovery' column to the tables of selected alleles.
        * An alert box is now shown when a data file is loaded that contains
          markers that have 'No data'.
        * Added 'Percentage of total reads' to the graph filtering options.
        * Added a note to the table filtering options to explain that the
          minimum percentage correction and recovery have an OR relation.
      ebf700a7
  5. 16 Nov, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Various fixes and improvements · 313867bc
      Hoogenboom, Jerry authored
      Fixed:
      * The 'to' base in variants called on mtDNA was incorrect. This bug could also cause FDSTools to crash.
      * FDSTools would crash if you tried to generate an allele name for a primer dimer of an mtDNA marker. (Now, you get an insane but entirely accurate allele name instead.)
      * Fixed bug that caused some perfectly valid mtDNA allele names to be rejected when attempting to convert them back to raw sequences.
      
      Improved:
      * You can now also specify the ending position of the markers in the FDSTools library. If you do, you may also additionally specify a second start position (and optionally also a second end position, and so on). FDSTools will interpret this as that the marker is the concatenation of each of these fragments. This was primarily introduced to support mtDNA fragments that contain (somewhere in the middle) the origin of mtDNA base numbering.
      * More helpful error message when format violations are detected while parsing the library file.
      * More helpful error message when the -e/--tag-expr regular expression could not be compiled.
      * Added a paragraph about sequence alignment caching to the help text of Seqconvert.
      * Added a 'flags' column to BGCorrect output, which gives information about the data that was used to do the correction.
      
      Background noise profiles:
      * Removed -C/--cross-tabular option from BGEstimate, BGPredict, and BGMerge and also removed the ability to read files in this format.
      * BGEstimate, BGHomStats, and BGPredict now add a column 'tool' with their name to the output.
      313867bc
  6. 04 Nov, 2015 1 commit
    • Hoogenboom, Jerry's avatar
      Implemented support for non-STR markers, improved file handling and more · 1083919c
      Hoogenboom, Jerry authored
      Additions and improvements to the FDSTools library file format:
      * New [genome_position] section in FDSTools-style library files allows
      for specifying the chromosome and position of each marker.
      * New [no_repeat] section in FDSTools-style library files allows for
      including non-STR markers.
      * Comma/semicolon/space-separated values in FDSTools-style library files
      can now also be separated by tab characters and multiple consecutive
      separators are no longer collapsed (with the exception of whitespace).
      * If no prefix and/or suffix has been specified for an alias, the
      prefix/suffix of the marker itself is used.
      * Implemented support for non-STR markers (e.g. SNP clusters) and mtDNA
      markers. Allele names of the latter follow mtDNA nomenclature.
      * Improved the logic of generating STR allele names for sequences that
      have a prefix or suffix sequence that was not included in the library
      file.
      * Updated and clarified various explanatory texts in generated FDSTools
      library files.
      
      Fixed:
      * Fixed a bug that caused prefix/suffix variants in aliases to go
      missing in allele names.
      
      Improved file handling:
      * Library files are now closed immediately after parsing them.
      * Sample data input files are opened one at a time now.
      
      Visualisations:
      * Updated Vega to version 2.3.1.
      * Worked around a bug in Google Chrome that caused the 'Save image' link
      to stop working after having been used once.
      1083919c
  7. 01 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Cleanup and minor enhancements · 03fc3d49
      jhoogenboom authored
      * BGCorrect and Stuttermark will now exit with an error message if
        more than one input file for the same sample is specified and no
        separate output files are given. Previously these tools would
        just overwrite the output file repeatedly, discarding the output
        of all but the last data file of the sample.
      * Removed to main() functions and related stubs from the tools
        because they are not actually runnable directly anyway.
      * Added some more help text to some of the tools.
      * Doubled the size of the marker name filter input element on the
        HTML visualisations.
      03fc3d49
  8. 21 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Profilevis, and various bug fixes · b7d64a4f
      jhoogenboom authored
      * New visualisation Profilevis added to the package, but not yet to
        the Vis tool.
      * The Vis tool now prints a helpful error message if no output file
        was specified, instead of printing half a megabyte of HTML and
        minified JavaScript to the terminal.
      * Fixed crash that occurred when attempting to convert the sequence
        of an alias to its allele name.
      * Fixed various bugs in the functions that convert sequences to
        TSSV-style and allele names. Only the conversion of non-matching
        sequences was affected.
      * Added "max_expected_copies" section to the FDSTools library
        format. The default value is 2. Allelefinder will now use these
        as the maximum number of alleles per marker if the
        -a/--max-alleles option is not specified.
      * The section headers in the FDSTools library format are now case
        insensitive.
      b7d64a4f
  9. 07 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Reworked input/output file arguments · 7f23c2e0
      jhoogenboom authored
      * All tools now write to stdout by default. Tools that support
        writing report files write those to stderr by default. The
        -o/--output and -r/--report options can be used to override
        these.
      * Tools that operated on one sample at a time (bgcorrect,
        seqconvert, stuttermark) now support batch processing. The new
        -i/--input argument takes a list of files. In batch mode,
        the -o/--output argument can be used to specify a list of
        corresponding output files (which must be the same length). It
        is also possible to specify a format string to automatically
        generate file names. -o/--output defaults to "\1-\2.out" which is
        automatically expanded to "sampletag-toolname.out". The old
        positional arguments [IN] and [OUT] are maintained and allow for
        conveniently running the tools on a single sample file.
        [IN] is mutually exclusive with -i/--input and [OUT] is mutually
        exclusive with -o/--output. [OUT] now also accepts the filename
        format, but when not in batch mode, it still defaults to stdout.
        Note that by default, the sample tag is extracted from the input
        filenames by simply stripping the extension. This means a minimal
        batch processing command like "fdstools stuttermark -i *.csv"
        automatically creates a "...-stuttermark.out" file next to each
        CSV file in the current working directory.
      * Libconvert now also supports only specifying an output file.
        This makes it easier to write the default FDSTools library to a
        new file. E.g., "fdstools libconvert mynewfile.txt" now creates
        "mynewfile.txt" if it does not exist, and writes the default
        library to it. Most helpful.
      7f23c2e0
  10. 06 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Greatly increased argument help · b30bdbbc
      jhoogenboom authored
      * All tools now have a longer description in the tool-specific help
        page.
      * Arguments are now presented in groups and the order is the same
        across tools.
      
      Furthermore:
      * Fixed bug that rendered BGHomStats and BGEstimate with the -H
        option useless.
      * The report of Allelefinder and BGEstimate is now written to
        sys.stderr by default. This means the report is now always
        generated (but it may be sent directly to /dev/null explicitly by
        the user). The big plus is that the progress of the tools is
        visible in the terminal when the tools are run by hand.
      b30bdbbc
  11. 04 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Blame · 8685a304
      jhoogenboom authored
      * New tool Blame can be used to find particularly dirty samples and
        to construct a DNA profile of the contaminator.
      * Fixed bug BGCorrect that resulted in incorrect values in the
        *_add columns.
      * BGEstimate and BGHomStats no longer crash if a library file is
        provided.
      * SeqConvert can now use a different library file for the output,
        thereby offering some possibilities to update allele names when a
        library file gets updated.
      * Replaced various uses of map() by generator expressions and
        listcomps for increased readability speed (although slightly).
      8685a304
  12. 31 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Various FDSTools-wide enhancements · 7b12cccb
      jhoogenboom authored
      * Unknown arguments are now silently ignored. If this results in
        the tool not being able to run, the usage information of the tool
        is printed instead of the general fdstools usage.
      * Seqconvert no longer crashes on an empty line in the input.
      * Libconvert now maintains the order of prefix/suffix sequences.
      * Allele names with aliases other than 'X' or 'Y' are now correctly
        recognised. These were previously rejected as 'unknown format'.
      * Fixed bug where a prefix/suffix other than the first listed in
        the library file was sometimes used as the canonical sequence.
      * Sequence format conversion from raw to TSSV-style sequences now
        attempts to match the prefix, suffix, and STR pattern to
        non-matching sequences on a best effort basis. This is
        especially useful when converting to allelenames (which is done
        via TSSV-style sequences), since it results in an allele name
        that matches more closely the names of other alleles.
      * Generating allele names for sequences that lack a prefix and/or
        suffix is now supported (by adding a variant description that
        deletes the entire prefix/suffix).
      7b12cccb
  13. 24 Jul, 2015 1 commit
  14. 23 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Laying foundations · 160594c5
      jhoogenboom authored
      * Introducing a new, extended library file format to support
        allele name generation.  The new libconvert tool can convert
        TSSV libraries to the new format and vice versa.
      * Added functions for converting between raw sequences, TSSV-style
        sequences, and allele names.
      * Added global -d/--debug option.
      
      Stuttermark updates:
      * Stuttermark now automatically converts input sequences to
        TSSV-style if a library is provided.
      * Stuttermark will no longer crash if there is no 'name' column.
        Instead, all sequences are taken to belong to the same marker.
      
      New tools:
      * libconvert converts between FDSTools and TSSV library formats.
      * seqconvert converts between raw sequences, TSSV-style sequences,
        and allele names.
      * allelefinder detects the true alleles in reference samples.
      160594c5