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. 03 Aug, 2015 1 commit
    • jhoogenboom's avatar
      Introducing BGHomStats · a09131d9
      jhoogenboom authored
      * New tool BGHomStats computes statistics (minimum, maximum, mean,
        and sample variance) of noise ratios in homozygous samples.
      * The default BGEstimate output format has been changed to be
        compatible with that of BGHomStats. The cross-tabular output
        format is still available as an option because it easily uses 90%
        less disk space. BGCorrect (and other future tools that use noise
        profiles) will work with both formats.
      * Fixed bug in the --min-samples option of BGEstimate that could
        cause some alleles with less than the specified number of samples
        to be included if --drop-samples is used at the same time.
      * The user now receives an error message if there are unknown
        arguments. The error message lists the usage string of the
        requested tool. (Argparse's default was to print the general
        FDSTools usage string, which is not helpful.)
      a09131d9
  4. 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
  5. 30 Jul, 2015 1 commit
  6. 29 Jul, 2015 1 commit
    • jhoogenboom's avatar
      Introducing bgestimate · be745e64
      jhoogenboom authored
      I could write about all its features here, but instead I will point
      out some future plans to highlight the things that are possibly not
      optimal in their current implementation.
      
      There are a number of things I plan to change in the future:
      * The output format is currently JSON, perhaps a carefully designed
        tabular format is a better choice. The benefit of switching to a
        tabluar format is that the data can be loaded into e.g. Excel as
        well.
      * The profiles are currently produced separately for forward and
        reverse reads. I would prefer to integrate these into a single
        computation that estimates allele balance in the heterozygotes
        using both strands as well.
      * I would like to add information about strand bias of the alleles
        as well. The most straightforward way to do this is to set only
        the forward reads of the true allele to 100 and treat the reverse
        reads the same as all background products. You will then obtain a
        number of reverse reads observed for ever 100 forward reads of
        the true allele.
      * I think it would be appropriate to make sure the values in the
        allele balance matrices of each sample ('Ax' in the source code)
        should add up to 1. For homozygotes, it is currently a scalar 1,
        the sum of the elements tend to be more than 1. This means that a
        heterozygous sample has a stronger influence on the profiles than
        a homozygous sample.
      be745e64
  7. 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
  8. 24 Jul, 2015 1 commit
  9. 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
  10. 02 Jul, 2015 2 commits