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Can someone please explain how the SOAP2 options -v and -M interact? The online help is pasted below but I don't
understand. For example, if I set -v 2 and also -M 1, do my alignments allow 2 mismatches or one mismatch? What does it mean in the description of -M where it says "shouldn't contain more than 2 mismatches"? Does that mean I cannot set -v to a number larger than 2?
The help file says:
-v INT Totally allowed mismatches in one read, [2]
-M INT Match mode for each read or the seed part of read, whichshouldn't contain more than 2 mismaches, [4]