dont put haplotypes in ReferencePathOverlays#236
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glennhickey merged 2 commits intomasterfrom Feb 6, 2026
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adamnovak
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Feb 5, 2026
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I think the idea of "hidden" paths needs to be removed, since they don't exist anymore (and that's what was causing the over-indexing). But it looks like this will fix the over-indexing.
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| /// even if they are hidden. | ||
| ReferencePathOverlay(const PathHandleGraph* graph, bool all_paths = false); | ||
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| /// Same, but also indexes hidden paths listed in extra_path_names. |
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We don't/shouldn't have a concept of a path being "hidden" anymore.
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| const std::unordered_set<std::string>& extra_path_names, | ||
| bool all_paths = false); |
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If all_paths is true, extra_path_names can't really be used, because we'll do all paths, since none of them are hidden anymore.
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| // TODO: If we made the overlay transparent so we could access paths | ||
| // that didn't get indexed, we wouldn't be weirdly indexing haplotype | ||
| // paths from backends that don't hide them in the "reference" path | ||
| // overlay. |
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Now all the backends are like that; I think I forgot to address that here when I made that change.
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Let's keep ReferencePathOverlays for Reference Paths. Otherwise, memory can get out of hand on larger graphs...