support gapped kmers

[notestaff]

@marekkokot It would be great if you could support gapped kmers. The only change is in extracting kmers from reads. E.g. for 4-mers with a 2-base gap in the middle, from the read TCGATCGATCGA you'd extract TCTC CGCG GAGA etc . So there would be just one extra parameter, the gap size. This would help identify additional sequence similarities where differences between sequences prevent them from sharing identical ungapped kmers.