• Hoogenboom, Jerry's avatar
    Allelefinder fixes and mtDNA allele naming · e30c0408
    Hoogenboom, Jerry authored
    Fixed:
    * The -c/--stuttermark-column option of Allelefinder was not filtering
      out the non-ALLELE sequences as it was supposed to. (This issue was
      introduced in ce7f34fb, in which a bug was fixed that caused this
      option to filter all sequences, including the ones marked with ALLELE.
      So it turns out this option has been broken since 732e83ba.)
    
    Improved:
    * Allelefinder will no longer reject a marker based on the number of
      reads of 'Other sequences'.
    * Adjusted sequence alignment parameters for mtDNA sequences to produce
      allele names that more closely follow historical mtDNA mutation
      nomenclature.
    e30c0408
allelefinder.py 9.18 KB