Version 3.5.0

Summary of changes:

• Update minimap2 command used in read realignment (turn off homopolymer compression to avoid occasional odd indels).
• Improve handling of long deletions in phasing.
• Add genes_in_region field in JSON output to list genes encoded in each region (pseudogenes excluded).
• Add an annotation script as a proof-of-concept for how to annotate variants downstream of Paraphase.