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Previously, `Machine::liftover()` returned a flat list of `ContiguousIntervalPair`s with no information about which chain each segment originated from. This made it impossible to distinguish between segments from different chains covering the same region (ambiguous mapping) and segments from the same chain separated by a gap (straddle). - `Machine::liftover()` now returns `Vec<LiftoverResult>`, where each `LiftoverResult` groups the segments from a single chain together with the full chain header. - `LiftoverResult` exposes `.chain()` (returning the `alignment::section::header::Record`) and `.segments()`. - The builder now validates that no two chain sections share the same ID with inconsistent headers, erroring via `Error::DuplicateChainId` at build time.
Replaces hand-written `Display` and `std::error::Error` impls across the crate with `#[derive(Error)]` and `#[error(...)]` attributes. Also bumps the MSRV to 1.83.0 (required by `thiserror` v2), fixes a pre-existing clippy lint in `compare-crossmap`, and updates the binary to use the new `LiftoverResult` API.
When multiple chains overlap the same single-position query, the comparison binary now selects the result from the highest-scoring chain rather than asserting that only one chain matched. This aligns with how `CrossMap` resolves ambiguous mappings.
Also bumps MSRV to 1.85.0 for `clap` 4.6.0 compatibility.
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Previously,
Machine::liftover()returned a flat list ofContiguousIntervalPairs with no information about which chain each segment originated from. This made it impossible to distinguish between segments from different chains covering the same region (ambiguous mapping) and segments from the same chain separated by a gap (straddle).Machine::liftover()now returnsVec<LiftoverResult>, where eachLiftoverResultgroups the segments from a single chain together with the full chain header. This lets callers trivially distinguish ambiguous mappings (results.len() > 1) from straddle splits (results[0].segments().len() > 1).The builder also now validates at build time that no two chain sections share the same ID with inconsistent headers, surfacing a
DuplicateChainIderror rather than silently dropping metadata at query time.All hand-written
Displayandstd::error::Errorimpls across the crate have been replaced withthiserrorderives. Thecompare-crossmapbinary now selects the highest-scoring chain when multiple chains overlap a single-position query (matching CrossMap's behavior) and logs timing information for both tools. MSRV has been bumped to 1.85.0.Before submitting this PR, please make sure:
cargo testandcargo clippy).CHANGELOG.md.