Support symbolic alternate <*> and <NON_REF> as NO_VARIATION

[j-coll]

There are mainly two ways to represent a reference block in a VCF:

Illumina

chr1   100    A    .    END=150    GT:DP    0/0:50

GATK

chr1   100    A    <NON_REF>    END=150     GT:DP:AD    0/0:50:49,1

The GATK way allows more detail in some fields that depend on the number of alleles, like AD. It is also possible to see combinations in multi-allelic variants:

chr1   100    A    C,<NON_REF>    .     GT:DP:AD    0/1:50:29,20,1

Also, this is almost the same solution proposed by the VCF4.3, which only changes the symbolic alternate with <*>

Normalize

1. The normalization should replace the alternate <NON_REF> with <*> to follow the VCF specification.
2. The normalizer, when splitting multi-allelic variants, should not generate variants with this allele as the main allele

Merge

When merging a variant with this type of reference block, it should add a new secondary alternate

Tasks

• Improve VariantBuilder::inferType to recognize <NON_REF> and <*> as NO_VARIATION
• In the VariantNormalizer, normalize the alternate <NON_REF> into <*>
• In the VariantNormalizer, when splitting a variant, do not generate the variant with <*> as main alternate
• In the VariantMerger, if a variant overlaps with a symbolic NO_VARIATION, add it as a secondary alternate