Ho do we handle these variants?

Example Alignment
position: 1 2 3 4 5 6 7 - 8 9
sequence:   A T G - - C A T

Variant partially overlapping read start
1 TA CGG

Variant partially overlapping read end
8 TG C

Partially missing Variant
4 GCA ATT

Totally missing Variant
5 GC ATG

Overlapping variants
2 AT C
3 TG AAA

Variant over an insertion
7 C G
