Allelefinder fixes and mtDNA allele naming
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.
Showing with 11 additions and 6 deletions