Convert chromosomal coordinates to contig coordinates

Question

[Peter Leontev]

Hello

I have a lot of point coordinates (let's say for SNPs) for the chromosomes of Apis Mellifera genome. What I want to do is to convert them to contig coordinates.

For example, SNP is at 5 nucleotide in the chromosome #1. It means one can represent contig coordinate of such SNP as 5th nucleotide in the contig #1 of the same chromosome (of course, if the length of the contig #1 > 5).

Another example: SNP is at 1000 nucleotide in chromosome #1. I want to get the same thing. However, here may be the problem that there are gaps (fortunately, lengths are known) between the contigs and it raises the question:

Is there right way to calculate contig coordinate of given SNP?

Thank you