Split isValidMM into two steps

[mweyrich28]

Right now, isValidMM returns a bool and also in cooperates the mm into the read match result.

But if we do a left/right extension, mms are added one after an other until the mm is no longer valid (due to either global threshold or local threshold).
In this case, the extension won't be appended to the readMatchResult.
But the mms were already added, meaning the result looks like this f.e.:

Read [20, 150]
Geno [400, 530]
MMs [13,14,15,16,17,18,19, 100]

-> so the strategy should be:

1. Keep track of mms in a separate list during extension
2. only if after complete extension, the impliedMMs + alread existing mms < threshold
3. append mms and append regions

I already applied a similar logic to the gap filling mechanic and diagonal filling.
But in l/r extension this is still not handeled.