Silent.aa_pos wrong for synonymous SNPs

[joaoe]

Hi.
Testcase over transcript ENSMUST00000086738

##fileformat=VCFv4.1
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

# The coding sequence around the variants
# ATG GAT TCT GTA CCA AGA CTG ACC AGC ATT TTG
#                       ^ 99772782
#  M   D   S   V   P   R   L   T   S   I   L

# Synonymous substition, 3rd nucleotide in codon
# AGA -> AGG (R/R)
chr1	99772782	.	A	G	5000	.	.	.

# Synonymous substition, 1st nucleotide in codon
# CTG -> TTG (L/L)
chr1	99772783	.	C	T	5000
	.	.	.
# CTG -> CXG [There are no synonymous nucleotide substitutions in the middle of the codon]
# chr1	99772784	.	T	X	5000	.	.	.

# All mixed
# AGA CTG -> AGG TTG (RL/rl)
chr1	99772782	.	AC	GT	5000	.	.	.

The three annotations for these cases should be

Silent(aa_pos=5, aa_ref=R)
Silent(aa_pos=6, aa_ref=L)
Silent(aa_pos=5, aa_ref=RL)

instead all the aa_pos properties are incremented by one.

The culprit is this line. aa_mutation_start_offset has been increased to skip the common prefix on aa_ref and aa_altafter the call to trim_shared_flanking_strings.
So, the argument being passed should be aa_mutation_start_offset - n_aa_shared.

[joaoe]

Btw, I think it makes sense to break apart the previous if because if aa_mutation_start_offset > reference_protein_length is True and n_aa_alt is not zero, then the mutation type should be ThreePrimeUTR right ?