• 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
lib.py 32.4 KB