-v and -M options

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DZS

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Dec 5, 2014, 11:42:08 AM12/5/14
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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, which shouldn't contain more than 2 mismaches, [4]

0: exact match only

1: 1 mismatch match only

2: 2 mismatch match only

3: [gap] (coming soon)

4: find the best hits



Thank you!

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