Add "intergenic" consequence

[holtgrewe]

Is your feature request related to a problem? Please describe.
We currently annotate variants on transcripts, intronic, upstream, and downstream. However, we don't annotate intergenic variants.

Describe the solution you'd like
Annotate intergenic variants as such intergenic_variant.

Describe alternatives you've considered
N/A

Additional context

• http://www.sequenceontology.org/miso/current_svn/term/SO:0001628

[tedil]

The SO term is available and annotated only if there are no overlapping transcripts found, see

mehari/src/annotate/seqvars/csq.rs

Lines 197 to 222 in bfd396b

	// Handle case of no overlapping transcripts -> intergenic.
	if txs.is_empty() {
	return Ok(Some(self.filter_ann_fields(vec![AnnField {
	allele: Allele::Alt {
	alternative: var.alternative.clone(),
	},
	gene_id: "".to_string(),
	consequences: vec![Consequence::IntergenicVariant],
	putative_impact: crate::annotate::seqvars::ann::PutativeImpact::Modifier,
	feature_type: FeatureType::Custom {
	value: "Intergenic".to_string(),
	},
	feature_id: "".to_string(),
	feature_biotype: vec![FeatureBiotype::Noncoding],
	rank: None,
	distance: None,
	strand: 0,
	hgvs_t: None,
	hgvs_p: None,
	tx_pos: None,
	cds_pos: None,
	protein_pos: None,
	gene_symbol: "".to_string(),
	messages: None,
	}])));
	}