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.