The actual genotypes are the same between gatk.vcf and
gatk_ref_alt_changed.vcf, but the REF, ALT and corresponding genotype
calls differ. This is to test if the conversion of genotype call
(e.g. 1/3) to the actual genotype (e.g. A/T) is working as intended.

Since it is not clear how we should handle non-diploid calls, we check
if variants are haploid/polyploid and error out if this is the case.

Before, we would iterate over decomposed called variants until we found
the variant where the REF and ALT matched the one in the positive vcf.
However, this meant that sites where the called vcf had different ALTs
could not be processed.

To resolve this, we had to drop support for decomposed variants.

Since it is not clear how we should handle phased calls, we check if the
variants are phased and error out if this is the case.

Previously we used cyvcf2 gt_types, which indicate whether a site is
hom_ref, heterozygous, hom_alt or unknown. A limitation of this approach
is that it only makes sense when the two vcf files have the same REF and
ALT alleles for a given position.

If this was not the case, vtools would silently skip the variant.
However, even when the ALT alleles are different between two vcf files,
the actual genotypes can still be compared. This was implemented in this
commit, which also fixes issue #8.

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