1. 01 Sep, 2015 1 commit
    • jhoogenboom's avatar
      Various bug fixes and additions · ce7f34fb
      jhoogenboom authored
      Fixed:
      * Fixed crash that would occur when an empty sequence (primer dimer) is converted from raw to TSSV-style (or allelename) format.
      * Fixed bug in BGHomRaw that caused incorrect sample tags in the output.
      * Fixed bug that caused allele names with negative CE numbers and names of primer dimers to be regarded as 'invalid allele names' even though FDSTools generated those names itself.
      * Fixed crash when reading sample data while looking for an annotation column.
      * Fixed bug in Allelefinder resulting in the complete absence of output that occurred when a column name with Stuttermark output was specified.
      
      Changed:
      * Restyled the Options box on HTML visualisations. It is now less transparent and oriented more vertically to reduce overlap with the visualisation. Options are now presented in groups.
      * Updated Vega to version 2.2.1.
      
      New:
      * Added *_corrected columns to BGCorrect output for convenience. E.g., the total_corrected column contains the value of total-total_noise+total_add.
      * Added -L/--log-scale option to the Vis tool.
      ce7f34fb
  2. 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
  3. 14 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing Samplevis · 300549e0
      jhoogenboom authored
      * New visualisation Samplevis visualises sample data files.
        (Note: visualisations are currently stored in the package, but
        are not available via FDSTools commands yet. A new tool is going
        to be introduced later, which will copy the visualisation files
        to a user-selected folder.)
      * Including the current versions of Vega and D3 for completeness.
      * Fixed missing numpy dependency in setup.py.
      * Clarified some option help texts in Allelefinder based on
        feedback by Rick and Kris.
      300549e0
  4. 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
  5. 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
  6. 05 Aug, 2015 1 commit
  7. 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
  8. 30 Jul, 2015 1 commit
  9. 27 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Updates to allelefinder · f9543ed9
      jhoogenboom authored
      * Allelefinder can now combine data from multiple files into a
        single sample (this happens when the same sample tag was
        extracted from their names).
      * Allelefinder can now automatically convert sequences to a given
        format (this is optional though). This is particularly useful
        when combining the knownalleles.csv and newalleles.csv files of
        a sample. (Note that allelefinder still assumes that the files
        contain different alleles; no attempt is made to check whether
        the same allele was represented in multiple files.)
      f9543ed9
  10. 24 Jul, 2015 1 commit
  11. 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