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…tars-core Migrates 10 structural methods (trim, shift, flank, resize, narrow, promoters, reduce, concat, disjoin, gaps) plus pintersect as inherent methods on RegionSet in gtars-core. Introduces IntervalSetOps trait in core with sweep-line implementations for RegionSet covering two-set operations: setdiff, intersect, union, jaccard, coverage, overlap_coefficient, subtract, closest, cluster. Strips IntervalRanges trait in genomicdist down to only intersect_all (the one method requiring an overlap index). Moves SortedRegionSet to core with re-export from genomicdist. Updates all downstream callers (CLI, Python, WASM, R bindings, examples) to use the new locations.
…query methods MCO now owns its source RegionSet via from_region_set() constructor, eliminating the error-prone pattern of passing source as a parameter. Implements IntervalSetOps trait (delegating to owned source) so callers can write generic code over impl IntervalSetOps. Adds MCO-only query methods: subset_by, count_overlaps, any_overlaps, find_overlaps_indexed, intersect_all. Moves intersect_all from genomicdist to MCO (genomicdist now delegates). Old method names kept as deprecated aliases.
Remove the RegionSetOverlaps extension trait which was redundant indirection now that MultiChromOverlapper has inherent query methods. Update Python bindings to build an MCO index explicitly instead of calling trait methods on RegionSet.
Remove the now-empty IntervalRanges trait and interval_ranges.rs file. The strand-aware StrandedRegionSet methods (promoters, reduce, setdiff) move to inherent methods in models.rs alongside the struct definitions. The intersect_all convenience on RegionSet is replaced by direct MCO usage in downstream crates. All IntervalRanges imports removed from CLI, WASM, Python, and R bindings.
Last remaining reference to the deleted IntervalRanges trait was a test class name in gtars-python.
Resolve conflict: interval_ranges.rs deleted on this branch, modified on dev (PR #244 closest() fix + R cast safety). The closest() improvements are already in RegionSet::closest(). R/WASM safe-cast changes from dev merge cleanly.
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Resolves the index-reuse problem. Callers can now build a
MultiChromOverlapperonce and reuse it across multiple query/set-algebra operations instead of rebuilding the AIList index every time.closest,cluster,union,subtract, etc.) moved from extension traits to inherent methods onRegionSetRegionSetand gets index-nativeIntervalSetOpsplus query methods (subset_by,intersect_all,count_overlaps, etc.)IntervalRangesandRegionSetOverlapsclosest()bug where a fixed ±2 window missed long intervalsThis is not considered "finished" and "final", but more of a step forward. So, happy for things to continue to change. but his is helping me conceptualize this.