Small variant and SV phasing

[Madelinehazel]

Add annotation to indicate if there are rare SVs in the same gene as a rare small variant and what their phase is, and vice versa. Ex:

Position	Ref	Alt	Gene	Phased_GT	Phase_set	Second_hit	Phase
chr1:100877893	T	C	EXTL2	0|1	phase set ID 1	Variant.ID.1; Variant.ID.2; Variant.ID.3	cis;trans;unphased
chr1:1014228	G	A	ISG15	1|0	phase set ID 2	.	.

Only consider rare ( less than 5% in CMH) variants.