Consider circularity when finding intra-contig breakpoints #28
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…ferently depending on whether the contig is curcular
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Leaving this as draft for now because I don't have time to add a test case. |
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@tfenne tests added, ready for review |
tfenne
approved these changes
Oct 6, 2023
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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.starttoseg1.range.start < seg2.range.endfor the negative strand comparison.