There are two ways in which a variant can be no call. The variant can be
present in the vcf file with a ./. genotype, or the variant can be
missing from the vcf file altogether. This commit adds a test case to
verify that no call sites are counted properly when they are missing
from the called vcf file.

Sites that are missing from the positive vcf file do not count towards
alleles_no_call, since we do not care about variants which are not
present in the positive vcf file.

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.

Devel

This is also the default behaviour in master. This change restores
the default behaviour, while still preserving the option to write
the stats json directly to a file by specifying --stats.

Add docs

See merge request !3

Use logarithmic mean.

See merge request !1

slight refactor

See merge request !2