Properly count 'no call' sites

cyvcf2 assigns 'no call' sites a DP and QC of -1, which caused the
statistics to be off since we checked for 'no call' sites (i.e. gt=3)
after all other checks.

The check for 'no call' sites was moved up to make sure only true sites
get to the QC/DP checks. Furthermore, the QC/DP checks are counted
independenly, since a site can fail multiple checks.

The test cases were updated to reflect these changes, and now all pass.