• 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
lib.py 59.8 KB