• 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
bghomraw.py 7.86 KB