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cram/record/feature: Use named fields
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@zaeleus
zaeleus committed Oct 5, 2024
1 parent 02c5340 commit ebb6c81
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Showing 10 changed files with 746 additions and 342 deletions.
63 changes: 32 additions & 31 deletions ...ram/src/data_container/compression_header/preservation_map/substitution_matrix/builder.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,15 @@ pub struct Builder {
impl Builder {
pub fn update(&mut self, record: &Record) {
for feature in record.features().iter() {
match feature {
Feature::Substitution(_, substitution::Value::Bases(reference_base, read_base)) => {
self.histogram.hit(*reference_base, *read_base);
if let Feature::Substitution { value, .. } = feature {
match value {
substitution::Value::Bases(reference_base, read_base) => {
self.histogram.hit(*reference_base, *read_base);
}
substitution::Value::Code(_) => {
panic!("substitution matrix cannot be built from substitution codes");
}
}
Feature::Substitution(_, substitution::Value::Code(_)) => {
panic!("substitution matrix cannot be built from substitution codes");
}
_ => {}
}
}
}
Expand Down Expand Up @@ -51,30 +52,30 @@ mod tests {
.set_read_length(bases.len())
.set_bases(bases)
.set_features(Features::from(vec![
Feature::Substitution(
Position::try_from(1)?,
substitution::Value::Bases(Base::A, Base::T),
),
Feature::Substitution(
Position::try_from(3)?,
substitution::Value::Bases(Base::A, Base::T),
),
Feature::Substitution(
Position::try_from(6)?,
substitution::Value::Bases(Base::A, Base::C),
),
Feature::Substitution(
Position::try_from(7)?,
substitution::Value::Bases(Base::A, Base::G),
),
Feature::Substitution(
Position::try_from(9)?,
substitution::Value::Bases(Base::A, Base::G),
),
Feature::Substitution(
Position::try_from(10)?,
substitution::Value::Bases(Base::A, Base::T),
),
Feature::Substitution {
position: Position::try_from(1)?,
value: substitution::Value::Bases(Base::A, Base::T),
},
Feature::Substitution {
position: Position::try_from(3)?,
value: substitution::Value::Bases(Base::A, Base::T),
},
Feature::Substitution {
position: Position::try_from(6)?,
value: substitution::Value::Bases(Base::A, Base::C),
},
Feature::Substitution {
position: Position::try_from(7)?,
value: substitution::Value::Bases(Base::A, Base::G),
},
Feature::Substitution {
position: Position::try_from(9)?,
value: substitution::Value::Bases(Base::A, Base::G),
},
Feature::Substitution {
position: Position::try_from(10)?,
value: substitution::Value::Bases(Base::A, Base::T),
},
]))
.build();

Expand Down
16 changes: 8 additions & 8 deletions noodles-cram/src/data_container/slice.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -649,10 +649,10 @@ mod tests {
.set_reference_sequence_id(0)
.set_read_length(2)
.set_alignment_start(Position::MIN)
.set_features(Features::from(vec![Feature::Bases(
Position::MIN,
vec![b'A', b'C'],
)]))
.set_features(Features::from(vec![Feature::Bases {
position: Position::MIN,
bases: vec![b'A', b'C'],
}]))
.build()];

resolve_bases(
Expand Down Expand Up @@ -681,10 +681,10 @@ mod tests {
.set_id(1)
.set_bam_flags(sam::alignment::record::Flags::empty())
.set_read_length(2)
.set_features(Features::from(vec![Feature::Scores(
Position::try_from(1)?,
vec![8, 13],
)]))
.set_features(Features::from(vec![Feature::Scores {
position: Position::try_from(1)?,
quality_scores: vec![8, 13],
}]))
.build(),
Record::builder().set_id(2).build(),
Record::builder()
Expand Down
41 changes: 27 additions & 14 deletions noodles-cram/src/io/reader/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -465,52 +465,65 @@ where
match code {
Code::Bases => {
let bases = self.read_stretches_of_bases()?;
Ok(Feature::Bases(position, bases))
Ok(Feature::Bases { position, bases })
}
Code::Scores => {
let quality_scores = self.read_stretches_of_quality_scores()?;
Ok(Feature::Scores(position, quality_scores))

Ok(Feature::Scores {
position,
quality_scores,
})
}
Code::ReadBase => {
let base = self.read_base()?;
let quality_score = self.read_quality_score()?;
Ok(Feature::ReadBase(position, base, quality_score))

Ok(Feature::ReadBase {
position,
base,
quality_score,
})
}
Code::Substitution => {
let code = self.read_base_substitution_code()?;
Ok(Feature::Substitution(position, code))
let value = self.read_base_substitution_code()?;
Ok(Feature::Substitution { position, value })
}
Code::Insertion => {
let bases = self.read_insertion_bases()?;
Ok(Feature::Insertion(position, bases))
Ok(Feature::Insertion { position, bases })
}
Code::Deletion => {
let len = self.read_deletion_length()?;
Ok(Feature::Deletion(position, len))
Ok(Feature::Deletion { position, len })
}
Code::InsertBase => {
let base = self.read_base()?;
Ok(Feature::InsertBase(position, base))
Ok(Feature::InsertBase { position, base })
}
Code::QualityScore => {
let score = self.read_quality_score()?;
Ok(Feature::QualityScore(position, score))
let quality_score = self.read_quality_score()?;

Ok(Feature::QualityScore {
position,
quality_score,
})
}
Code::ReferenceSkip => {
let len = self.read_reference_skip_length()?;
Ok(Feature::ReferenceSkip(position, len))
Ok(Feature::ReferenceSkip { position, len })
}
Code::SoftClip => {
let bases = self.read_soft_clip_bases()?;
Ok(Feature::SoftClip(position, bases))
Ok(Feature::SoftClip { position, bases })
}
Code::Padding => {
let len = self.read_padding_length()?;
Ok(Feature::Padding(position, len))
Ok(Feature::Padding { position, len })
}
Code::HardClip => {
let len = self.read_hard_clip_length()?;
Ok(Feature::HardClip(position, len))
Ok(Feature::HardClip { position, len })
}
}
}
Expand Down
30 changes: 17 additions & 13 deletions noodles-cram/src/io/writer/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -501,41 +501,45 @@ where
self.write_feature_position(position)?;

match feature {
Feature::Bases(_, bases) => {
Feature::Bases { bases, .. } => {
self.write_stretches_of_bases(bases)?;
}
Feature::Scores(_, quality_scores) => {
Feature::Scores { quality_scores, .. } => {
self.write_stretches_of_quality_scores(quality_scores)?;
}
Feature::ReadBase(_, base, quality_score) => {
Feature::ReadBase {
base,
quality_score,
..
} => {
self.write_base(*base)?;
self.write_quality_score(*quality_score)?;
}
Feature::Substitution(_, value) => {
Feature::Substitution { value, .. } => {
self.write_base_substitution_code(*value)?;
}
Feature::Insertion(_, bases) => {
Feature::Insertion { bases, .. } => {
self.write_insertion(bases)?;
}
Feature::Deletion(_, len) => {
Feature::Deletion { len, .. } => {
self.write_deletion_length(*len)?;
}
Feature::InsertBase(_, base) => {
Feature::InsertBase { base, .. } => {
self.write_base(*base)?;
}
Feature::QualityScore(_, score) => {
self.write_quality_score(*score)?;
Feature::QualityScore { quality_score, .. } => {
self.write_quality_score(*quality_score)?;
}
Feature::ReferenceSkip(_, len) => {
Feature::ReferenceSkip { len, .. } => {
self.write_reference_skip_length(*len)?;
}
Feature::SoftClip(_, bases) => {
Feature::SoftClip { bases, .. } => {
self.write_soft_clip(bases)?;
}
Feature::Padding(_, len) => {
Feature::Padding { len, .. } => {
self.write_padding(*len)?;
}
Feature::HardClip(_, len) => {
Feature::HardClip { len, .. } => {
self.write_hard_clip(*len)?;
}
}
Expand Down
40 changes: 29 additions & 11 deletions noodles-cram/src/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -338,11 +338,11 @@ pub(crate) fn calculate_alignment_span(read_length: usize, features: &Features)
features
.iter()
.fold(read_length, |alignment_span, feature| match feature {
Feature::Insertion(_, bases) => alignment_span - bases.len(),
Feature::InsertBase(_, _) => alignment_span - 1,
Feature::Deletion(_, len) => alignment_span + len,
Feature::ReferenceSkip(_, len) => alignment_span + len,
Feature::SoftClip(_, bases) => alignment_span - bases.len(),
Feature::Insertion { bases, .. } => alignment_span - bases.len(),
Feature::InsertBase { .. } => alignment_span - 1,
Feature::Deletion { len, .. } => alignment_span + len,
Feature::ReferenceSkip { len, .. } => alignment_span + len,
Feature::SoftClip { bases, .. } => alignment_span - bases.len(),
_ => alignment_span,
})
}
Expand Down Expand Up @@ -370,15 +370,33 @@ mod tests {
let features = Features::default();
assert_eq!(calculate_alignment_span(4, &features), 4);

let features = Features::from(vec![Feature::HardClip(Position::try_from(1)?, 4)]);
let features = Features::from(vec![Feature::HardClip {
position: Position::try_from(1)?,
len: 4,
}]);
assert_eq!(calculate_alignment_span(4, &features), 4);

let features = Features::from(vec![
Feature::Insertion(Position::try_from(1)?, vec![b'A', b'C']),
Feature::InsertBase(Position::try_from(4)?, b'G'),
Feature::Deletion(Position::try_from(6)?, 3),
Feature::ReferenceSkip(Position::try_from(10)?, 5),
Feature::SoftClip(Position::try_from(16)?, vec![b'A', b'C', b'G', b'T']),
Feature::Insertion {
position: Position::try_from(1)?,
bases: vec![b'A', b'C'],
},
Feature::InsertBase {
position: Position::try_from(4)?,
base: b'G',
},
Feature::Deletion {
position: Position::try_from(6)?,
len: 3,
},
Feature::ReferenceSkip {
position: Position::try_from(10)?,
len: 5,
},
Feature::SoftClip {
position: Position::try_from(16)?,
bases: vec![b'A', b'C', b'G', b'T'],
},
]);
assert_eq!(calculate_alignment_span(20, &features), 21);

Expand Down
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