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.
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