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cram/record/sequence/iter: Move positions iterator to a module
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104 changes: 104 additions & 0 deletions
104
noodles-cram/src/record/sequence/iter/with_positions.rs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| use std::slice; | ||
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| use noodles_core::Position; | ||
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| use crate::record::Feature; | ||
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| pub(super) struct WithPositions<'r, 'c: 'r> { | ||
| features: slice::Iter<'r, Feature<'c>>, | ||
| reference_position: Position, | ||
| read_position: Position, | ||
| } | ||
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| impl<'r, 'c: 'r> WithPositions<'r, 'c> { | ||
| pub(super) fn new(features: &'r [Feature<'c>], alignment_start: Position) -> Self { | ||
| Self { | ||
| features: features.iter(), | ||
| reference_position: alignment_start, | ||
| read_position: Position::MIN, | ||
| } | ||
| } | ||
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| pub(super) fn positions(&self) -> (Position, Position) { | ||
| (self.reference_position, self.read_position) | ||
| } | ||
| } | ||
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| impl<'r, 'c: 'r> Iterator for WithPositions<'r, 'c> { | ||
| type Item = ((Position, Position), &'r Feature<'c>); | ||
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| fn next(&mut self) -> Option<Self::Item> { | ||
| loop { | ||
| let feature = self.features.next()?; | ||
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| let (reference_position_delta, read_position_delta) = match feature { | ||
| Feature::Bases { bases, .. } => (bases.len(), bases.len()), | ||
| Feature::Scores { .. } => continue, | ||
| Feature::ReadBase { .. } => (1, 1), | ||
| Feature::Substitution { .. } => (1, 1), | ||
| Feature::Insertion { bases, .. } => (0, bases.len()), | ||
| Feature::Deletion { len, .. } => (*len, 0), | ||
| Feature::InsertBase { .. } => (0, 1), | ||
| Feature::QualityScore { .. } => continue, | ||
| Feature::ReferenceSkip { len, .. } => (*len, 0), | ||
| Feature::SoftClip { bases, .. } => (0, bases.len()), | ||
| Feature::Padding { .. } => (0, 0), | ||
| Feature::HardClip { .. } => (0, 0), | ||
| }; | ||
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| let feature_position = usize::from(feature.position()); | ||
| let match_len = feature_position - usize::from(self.read_position); | ||
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| self.reference_position = self | ||
| .reference_position | ||
| .checked_add(match_len) | ||
| .expect("attempt to add with overflow"); | ||
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| self.read_position = self | ||
| .read_position | ||
| .checked_add(match_len) | ||
| .expect("attempt to add with overflow"); | ||
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| let positions = self.positions(); | ||
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| self.reference_position = self | ||
| .reference_position | ||
| .checked_add(reference_position_delta) | ||
| .expect("attempt to add with overflow"); | ||
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| self.read_position = self | ||
| .read_position | ||
| .checked_add(read_position_delta) | ||
| .expect("attempt to add with overflow"); | ||
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| return Some((positions, feature)); | ||
| } | ||
| } | ||
| } | ||
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| #[cfg(test)] | ||
| mod tests { | ||
| use super::*; | ||
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| #[test] | ||
| fn test_next() { | ||
| let features = [ | ||
| Feature::Bases { | ||
| position: Position::MIN, | ||
| bases: b"AC", | ||
| }, | ||
| Feature::Scores { | ||
| position: Position::MIN, | ||
| quality_scores: &[0, 0], | ||
| }, | ||
| ]; | ||
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| let mut iter = WithPositions::new(&features, Position::MIN); | ||
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| assert_eq!( | ||
| iter.next(), | ||
| Some(((Position::MIN, Position::MIN), &features[0])) | ||
| ); | ||
| assert!(iter.next().is_none()); | ||
| } | ||
| } |