findCAPs needs to be more flexible

[cflsjt]

Currently findCAPS expects ref and alt variant - singular.
expect 0/0 0/1 or 1/1
Some cases where I have:
1/1 1/2 2/2
Esp where ref can be different enough from genotypes being tested, such as when comparing polyploid tuberosum to phureja ref
Lost ~1000 out of 60,000 loci), lost targets and lost info.

Possible add for loop, variant1 variant2 etc output in CAPs file?