1. 05 Aug, 2015 1 commit
  2. 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
  3. 30 Jul, 2015 1 commit
  4. 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
  5. 24 Jul, 2015 1 commit
  6. 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