pave v1.6

Functional:

• keep splice effect for any phased variants
• HGVS coding for dups now shift position to duplicated bases
• handle phased missense and synonymous protein impacts
• phasing check for SNV/MNV overlap with inframe INDEL separately from frameshift count 2+
• favour protein duplications over inserts when considering realignment
• use stop-gained in HGVS protein instead of frameshift if has both

Bugs:

• check ref codon bases are valid in phasing routine, could cause crash if variant was at very end of exon with open reading frame
• fixed ref codon addition for overlaps in phasing logic

Technical:

• exit on thead error
• multi-threaded

Config:

• threads (default 1)
• removed gnomad_load_chr_on_demand