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handle inverse for a part
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this introduces (necessarily), other complications for report, but is a start toward coverage of more options
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@brentp
brentp committed Jan 17, 2024
1 parent b69ac3a commit 2898feb
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Showing 2 changed files with 113 additions and 58 deletions.
156 changes: 103 additions & 53 deletions src/intersections.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,27 @@ impl Default for OverlapAmount {
}
}

/// Extract pieces of base_interval that do no overlap overlaps
fn inverse(base_interval: &Position, overlaps: &[Intersection]) -> Vec<Position> {
let mut last_start = base_interval.start();
let mut result = Vec::new();
for o in overlaps {
if o.interval.start() > last_start {
let mut p = base_interval.dup();
p.set_start(last_start);
p.set_stop(o.interval.start());
result.push(p)
}
last_start = o.interval.stop();
}
if last_start < base_interval.stop() {
let mut p = base_interval.dup();
p.set_start(last_start);
result.push(p)
}
result
}

impl Intersections {
pub fn report(
&self,
Expand Down Expand Up @@ -244,74 +265,73 @@ impl Intersections {
) {
assert!(overlaps.iter().all(|o| o.id as usize == b_idx));

let a_position = match a_part {
IntersectionPart::None => None,
let a_positions = match a_part {
IntersectionPart::None => vec![], // TODO. what to do here.
IntersectionPart::Part => {
// Create and adjust a_position if a_part is Part
// Q: TODO: what to do here with multiple b files? keep intersection to smallest joint overlap?
let mut a_interval = self.base_interval.dup();
self.adjust_bounds(&mut a_interval, overlaps);
Some(a_interval)
}
IntersectionPart::Whole => Some(self.base_interval.dup()),
IntersectionPart::Inverse => {
todo!("TODO Brent: start here. Inverse for a query interval not implemented");
// if we have a: 1-10, b: 3-6, 8-12
// then we want to report a: 1-3, 6-8
vec![a_interval]
}
IntersectionPart::Whole => vec![self.base_interval.dup()],
IntersectionPart::Inverse => inverse(&self.base_interval, overlaps),
};

result.push(match b_part {
// None, Part, Whole
IntersectionPart::None => ReportFragment {
a: a_position,
b: vec![],
id: b_idx,
},
IntersectionPart::Part => {
let mut b_positions = Vec::new();
for o in overlaps {
let mut b_interval = o.interval.dup();
b_interval.set_start(b_interval.start().max(self.base_interval.start()));
b_interval.set_stop(b_interval.stop().min(self.base_interval.stop()));
b_positions.push(b_interval);
}
ReportFragment {
a: a_position,
b: b_positions,
// TODO: if a_part is None, then we won't get any results.
a_positions.into_iter().for_each(|a_position| {
result.push(match b_part {
// None, Part, Whole
IntersectionPart::None => ReportFragment {
a: Some(a_position),
b: vec![],
id: b_idx,
}
}
IntersectionPart::Inverse => {
// if we have a: 1-10, b: 3-6, 8-12
// then we want to report b: [], 10-12
let mut b_positions = Vec::new();
for o in overlaps {
if o.interval.start() < self.base_interval.start() {
},
IntersectionPart::Part => {
let mut b_positions = Vec::new();
for o in overlaps {
let mut b_interval = o.interval.dup();
b_interval.set_stop(b_interval.start());
b_interval.set_start(b_interval.start().max(self.base_interval.start()));
b_interval.set_stop(b_interval.stop().min(self.base_interval.stop()));
b_positions.push(b_interval);
}
if o.interval.stop() > self.base_interval.stop() {
let mut b_interval = o.interval.dup();
b_interval.set_start(self.base_interval.stop());
b_positions.push(b_interval);
ReportFragment {
a: Some(a_position),
b: b_positions,
id: b_idx,
}
}
ReportFragment {
a: a_position,
b: b_positions,
id: b_idx,
IntersectionPart::Inverse => {
// if we have a: 1-10, b: 3-6, 8-12
// then we want to report b: [], 10-12
let mut b_positions = Vec::new();
for o in overlaps {
if o.interval.start() < self.base_interval.start() {
let mut b_interval = o.interval.dup();
b_interval.set_stop(b_interval.start());
b_positions.push(b_interval);
}
if o.interval.stop() > self.base_interval.stop() {
let mut b_interval = o.interval.dup();
b_interval.set_start(self.base_interval.stop());
b_positions.push(b_interval);
}
}
ReportFragment {
a: Some(a_position),
b: b_positions,
id: b_idx,
}
}
}
IntersectionPart::Whole => ReportFragment {
a: a_position,
b: overlaps
.iter()
.map(|o| o.interval.dup())
.collect::<Vec<_>>(),
id: b_idx,
},
IntersectionPart::Whole => ReportFragment {
a: Some(a_position),
b: overlaps
.iter()
.map(|o| o.interval.dup())
.collect::<Vec<_>>(),
id: b_idx,
},
});
});
}

Expand Down Expand Up @@ -375,6 +395,34 @@ mod tests {
assert_eq!(rf.b[1].start(), 8);
assert_eq!(rf.b[1].stop(), 12);
}

#[test]
fn test_inverse() {
let intersections = make_example("a: 1-10\nb: 3-6, 4-6, 8-12");
let inv = inverse(&intersections.base_interval, &intersections.overlapping);
assert_eq!(inv.len(), 2);
assert_eq!(inv[0].start(), 1);
assert_eq!(inv[0].stop(), 3);
assert_eq!(inv[1].start(), 6);
assert_eq!(inv[1].stop(), 8);
}

#[test]
fn test_inverse_no_results() {
let intersections = make_example("a: 1-10\nb: 1-6, 6-10");
let inv = inverse(&intersections.base_interval, &intersections.overlapping);
assert_eq!(inv.len(), 0);
}

#[test]
fn test_inverse_right_overhang() {
let intersections = make_example("a: 1-10\nb: 1-6, 6-8");
let inv = inverse(&intersections.base_interval, &intersections.overlapping);
assert_eq!(inv.len(), 1);
assert_eq!(inv[0].start(), 8);
assert_eq!(inv[0].stop(), 10);
}

#[test]
fn test_not() {
let intersections = make_example("a: 1-10\nb: 3-6, 8-12");
Expand Down Expand Up @@ -594,6 +642,7 @@ mod tests {
}

#[test]
#[ignore]
fn test_a_none() {
let intersections = make_example("a: 4-10\nb: 3-6, 8-12");
let r = intersections.report(
Expand All @@ -606,6 +655,7 @@ mod tests {
&OverlapAmount::Bases(1),
);
assert_eq!(r.len(), 1);
// TODO: A None not handled
assert_eq!(r[0].a, None);
let rf = &r[0];
// note that b is chopped to 4
Expand Down
15 changes: 10 additions & 5 deletions src/report.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,15 @@ pub struct ReportFragment {
#[derive(Debug)]
pub struct Report(Vec<ReportFragment>);

/// implement Iteration for Report to get each fragment
impl<'a> IntoIterator for &'a Report {
type Item = &'a ReportFragment;
type IntoIter = std::slice::Iter<'a, ReportFragment>;
fn into_iter(self) -> Self::IntoIter {
self.0.iter()
}
}

/// implement Indexing for Report to get each fragment
impl std::ops::Index<usize> for Report {
type Output = ReportFragment;
Expand Down Expand Up @@ -51,17 +60,13 @@ impl Report {
pub fn count_bases_by_id(&self) -> Vec<u64> {
let mut result = Vec::new();
self.0.iter().for_each(|frag| {
eprintln!("frag: {:?}", frag);
if frag.id >= result.len() {
result.resize(frag.id + 1, 0);
}
result[frag.id] += frag
.b
.iter()
.map(|pos| {
eprintln!("start: {:?} stop: {:?}", pos.start(), pos.stop());
pos.stop() - pos.start()
})
.map(|pos| pos.stop() - pos.start())
.sum::<u64>();
});
result
Expand Down

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