Extract start and end positions from a PairwiseAlignment

[rohanmaddamsetti]

Hello, I have a feature request, that is related to some other open issues related to the API of this package.

Currently, there is no API to extract the start and end positions from a PairwiseAlignment. It would be great if the client can easily extract the location of matches (start, end) between the reference and the sequence of the PairwiseAlignment object.

Here is the hack that I wrote to solve this problem for myself, but it would be great if the API could expose an abstraction for locations of matches, or some analogous methods/functions so that the client doesn't have to mess with internal "private" fields.

function GetPairwiseAlignmentSeqStart(aln::PairwiseAlignment)
    return aln.a.aln.anchors[1].seqpos + 1
end

function GetPairwiseAlignmentRefStart(aln::PairwiseAlignment)
    return aln.a.aln.anchors[1].refpos + 1
end

function GetPairwiseAlignmentSeqEnd(aln::PairwiseAlignment)
    return aln.a.aln.anchors[end].seqpos
end

function GetPairwiseAlignmentRefEnd(aln::PairwiseAlignment)
    return aln.a.aln.anchors[end].refpos
end

Thanks for your consideration, hope this suggestion is helpful for both users as well as the designers and implementors of this package.

[CiaranOMara]

I believe the first and last reference positions are stored in Alignment. Two of the proposed functions might simplify to the following.

function firstref(aln::PairwiseAlignment)
    return aln.a.aln.firstref
end

function lastref(aln::PairwiseAlignment)
    return aln.a.aln.lastref
end