halAlignmentDepth with SNPs

[hy09]

Hi,

I was wondering if halAlignmentDepth would take snps into account. For example, with hal2maf, I got the alignment between human and chimp:

s	Homo_sapiens.chr13	71638838	10	+	114364328	AATGC**C**TTAC
s	Pan_troglodytes.CM009251.2	52882703	10	+	95599650	AATGC**T**TTAC

with the 1bp mismatch highlighted.

However when I use halAlignmentDepth on the same region, with human as the reference and chimp as the target I got:

 fixedStep chrom=chr13 start=71638839 step=1
1
1
1
1
1
1
1
1
1
1

My understanding is because the whole region is alignable, AlignmentDepth considers every single bp as alignable. Is this the expected behavior of halAlignmentDepth and is it possible to make it account for the SNPs (i.e. report 0 at the SNP location in this case)?

Thanks!