Consider circularity when finding intra-contig breakpoints

fulcrumgenomics / fgsv

Tools to gather evidence for structural variation via breakpoint detection.

MIT License

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Consider circularity when finding intra-contig breakpoints #28

Closed jdidion closed 1 year ago

jdidion commented 1 year ago

If the contig is circular, then we consider segment pairs where seg2.end < seg1.start (or seg1.end < seg2.start on the negative strand) to be normally oriented and calculate the distance between them relative to the origin.

I think I also fixed another bug (for the non-circular case), changing seg1.range.start < seg2.range.start to seg1.range.start < seg2.range.end for the negative strand comparison.

jdidion commented 1 year ago

Leaving this as draft for now because I don't have time to add a test case.

jdidion commented 1 year ago

@tfenne tests added, ready for review