Calculate position to exon/intron boundary

[pnrobinson]

For many applications, it would be useful to know the number of nucleotide residues that a variant is locatged away from the exon/intron boundary. This is basically just Delta (exon end, position). We need to consider if we want to take the absolute value of this distance or not--if we do not, then the sign of the distance encodes whether the distance is from the previous acceptor site (positive) or preceding the next donor site (negative).
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[holtgrewe]

I think we want to have the following:

• query is a function given transcript and genomic position
• result is a record {transcript, isExon, exonOrIntronNo, delta}
  • if is exon and delta > 0 then we are delta bases right of splice 5' junction of exon (delta = 1 is the first exon base)
  • if is exon and delta < 0 then we are delta bases left of splice 3' junction of exon (delta = -1 is the lastexon base)
  • if is not exon and delta > 0 then we are delta bases right of splice 5' junction of intron (delta = 1 is the first intron base)
  • if is not exon and delta < 0 then we are delta bases left of splice 3' junction of intron (delta = -1 is the last intron)

@pnrobinson please correct

I'll try to implement this small API addition for 0.23 together with stabilizing experimental dbNSFP/generic TSV/VCF support.

[jasiozaucha]

I would find this feature very useful as well. Please let me know when it's implemented.

[holtgrewe]

Postponing, will welcome tested PRs.

[pnrobinson]

If this is still open I will work on this.

[pnrobinson]

@ielis we have some of this functionality in other code. Can it be transferred easily to Jannovar as library code?