It is not quite clear, what to do, if the minimum appears multiple times in a submer, what is then the minimum? The first occurrence or all occurrences?
If I understand GetMinSubkmerPos in https://github.com/rcedgar/syncmer/blob/master/kmer.cpp correctly, then only the first occurrence is seen as minimum. Therefore, for an offset of 1 and k=4, s=2 the sequence AAAA would not be a syncmer.
It is not quite clear, what to do, if the minimum appears multiple times in a submer, what is then the minimum? The first occurrence or all occurrences?
If I understand GetMinSubkmerPos in https://github.com/rcedgar/syncmer/blob/master/kmer.cpp correctly, then only the first occurrence is seen as minimum. Therefore, for an offset of 1 and k=4, s=2 the sequence AAAA would not be a syncmer.