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//! This module provides an implementation of an AIList, but with a dynamic scaling for the number //! of sublists. //! ## Features //! - Extremely consistant. The way the input intervals are decomposed diminishes the effects of //! super containment. //! - Parallel friendly. Queries are on an immutable structure, even for seek //! - Consumer / Adapter paradigm, an iterator is returned. //! //! ## Details: //! //! Please see the [paper](https://www.biorxiv.org/content/10.1101/593657v1). //! //! Most interaction with this crate will be through the [`ScAIList`](struct.ScAIList.html)` struct //! The main methods is [`find`](struct.ScAIList.html#method.find). //! //! The overlap function for this assumes a zero based genomic coordinate system. So [start, stop) //! is not inclusive of the stop position for neither the queries, nor the Intervals. //! //! ScAIList is composed of four primary parts. A main interval list, which holds all the //! intervals after they have been decomposed. A component index's list, which holds the start //! index of each sublist post-decomposition, A component lengths list, which holds the length of //! each component, and finally a max_ends list, which holds the max end releative to a sublist up //! to a given point for each interval. //! //! The decomposition step is achieved by walking the list of intervals and recursively (with a //! cap) extracting intervals that overlap a given number of other intervals within a certain //! distance from it. The unique development in this implementation is to make the cap dynamic. //! //! # Examples //! //! ```rust //! use scailist::{Interval, ScAIList}; //! use std::cmp; //! type Iv = Interval<u32>; //! //! // create some fake data //! let data: Vec<Iv> = (0..20).step_by(5).map(|x| Iv{start: x, end: x + 2, val: 0}).collect(); //! println!("{:#?}", data); //! //! // make lapper structure //! let laps = ScAIList::new(data, None); //! assert_eq!(laps.find(6, 11).next(), Some(&Iv{start: 5, end: 7, val: 0})); //! //! let mut sim: u32= 0; //! // Calculate the overlap between the query and the found intervals, sum total overlap //! for i in (0..10).step_by(3) { //! sim += laps //! .find(i, i + 2) //! .map(|iv| cmp::min(i + 2, iv.end) - cmp::max(i, iv.start)) //! .sum::<u32>(); //! } //! assert_eq!(sim, 4); //! ``` use std::cmp::Ordering; /// This is the main object of this repo, see associated methods #[derive(Debug)] pub struct ScAIList<T: Clone + Eq + std::fmt::Debug> { /// The list of intervals intervals: Vec<Interval<T>>, // number of comps total num_comps: usize, // list of lengths of comps comp_lens: Vec<usize>, // start index's of comps comp_idxs: Vec<usize>, // vec of max ends, pairs with intervals max_ends: Vec<u32>, } /// Hold the start and stop of each sublist #[derive(Eq, Debug, Clone, Copy)] pub struct Interval<T: Clone + Eq + std::fmt::Debug> { pub start: u32, pub end: u32, pub val: T, } /// The ScAIList itself impl<T: Clone + Eq + std::fmt::Debug> ScAIList<T> { /// Create a new ScAIList out of the passed in intervals. The min_cov_len should probably be /// left as default, which is 20. It dictates how far ahead to look from a given point to /// determine if that interval covers enough other intervals to be moved to a sublist. The /// number of intervals it has to cover is equal to min_cov_len / 2. The number of sublists /// that might be fored is capped at intervals.len().log2(), but if there aren't many overlaps, /// fewer will be created. pub fn new(mut input_intervals: Vec<Interval<T>>, min_cov_len: Option<usize>) -> Self { let max_comps = (input_intervals.len() as f64).log2().floor() as usize + 1; let min_cov_len = min_cov_len.unwrap_or(20); // number of elements ahead to check for cov let min_cov = min_cov_len / 2; // the number of elemnts covered to trigger an extraction let num_comps; // number of components let mut comp_lens = vec![]; // lengths of each component let mut comp_idxs = vec![]; // start positions of each component let mut max_ends = vec![]; // list of the max end positions let min_comp_len = std::cmp::max(64, min_cov_len); // min length of a component let input_len = input_intervals.len(); input_intervals.sort(); let mut decomposed = vec![]; if input_len <= min_comp_len { num_comps = 1; comp_lens.push(input_len); comp_idxs.push(0); decomposed.append(&mut input_intervals); } else { let mut curr_comp = 0; while curr_comp < max_comps && input_len - decomposed.len() > min_comp_len { let mut list1 = vec![]; let mut list2 = vec![]; for i in 0..input_intervals.len() { let interval = &input_intervals[i]; let mut j = 1; let mut cov = 1; while j < min_comp_len && cov < min_cov && j + i < input_intervals.len() { if input_intervals[j + i].end >= interval.end { cov += 1; } j += 1; } if cov < min_cov { list1.push(input_intervals[i].clone()); } else { list2.push(input_intervals[i].clone()) } } // Add the component info to ScAIList comp_idxs.push(decomposed.len()); comp_lens.push(list1.len()); curr_comp += 1; if list2.len() <= min_comp_len || curr_comp == max_comps - 2 { // exit: add L2 to the end if !list2.is_empty() { decomposed.append(&mut list1); comp_idxs.push(decomposed.len()); comp_lens.push(list2.len()); decomposed.append(&mut list2); curr_comp += 1; } } else { decomposed.append(&mut list1); input_intervals = list2; } } num_comps = curr_comp; } // Augment with maxend for j in 0..num_comps { let comp_start = comp_idxs[j]; let comp_end = comp_start + comp_lens[j]; let mut max_end = decomposed[comp_start].end; max_ends.push(max_end); for iv in decomposed[comp_start + 1..comp_end].iter() { if iv.end > max_end { max_end = iv.end; } max_ends.push(max_end); } } ScAIList { num_comps, comp_idxs, comp_lens, max_ends, intervals: decomposed, } } /// Binary search to find the right most index where interval.start < query.stop #[inline] pub fn upper_bound(stop: u32, intervals: &[Interval<T>]) -> Option<usize> { let mut right = intervals.len(); let mut left = 0; if intervals[right - 1].start < stop { // last start pos is less than the stop, then return the last pos return Some(right - 1); } else if intervals[left].start >= stop { // first start pos > stop, not in this cluster at all return None; } while right > 0 { let half = right / 2; let other_half = right - half; let probe = left + half; let other_left = left + other_half; let v = &intervals[probe]; right = half; left = if v.start < stop { other_left } else { left } } // Guarded at the top from ending on either extreme if intervals[left].start >= stop { Some(left - 1) } else { Some(left) } } #[inline] pub fn iter(&self) -> IterScAIList<T> { IterScAIList { inner: self, pos: 0, } } #[inline] // TODO: Convert to a real iterator // TODO: Add seek... multiple cursors? how would that work? pub fn find(&self, start: u32, stop: u32) -> IterFind<T> { let mut result = vec![]; for comp_num in 0..self.num_comps { let comp_start = self.comp_idxs[comp_num]; let comp_end = comp_start + self.comp_lens[comp_num]; if self.comp_lens[comp_num] > 15 { let mut offset = match Self::upper_bound(stop, &self.intervals[comp_start..comp_end]) { Some(n) => n, None => continue, }; offset += comp_start; while offset >= comp_start && self.max_ends[offset] > start { if self.intervals[offset].end > start { result.push(&self.intervals[offset]); } offset = match offset.checked_sub(1) { Some(n) => n, None => break, }; } } else { for offset in comp_start..comp_end { if self.intervals[offset].start < stop && self.intervals[offset].end > start { result.push(&self.intervals[offset]); } } } } // Gather a list of starting points for each header IterFind { curr: 0, result } } } /// Find Iterator #[derive(Debug)] pub struct IterFind<'a, T: Clone + Eq + std::fmt::Debug> { curr: usize, result: Vec<&'a Interval<T>>, } impl<'a, T: Clone + Eq + std::fmt::Debug> Iterator for IterFind<'a, T> { type Item = &'a Interval<T>; #[inline] fn next(&mut self) -> Option<Self::Item> { if self.curr < self.result.len() { self.curr += 1; Some(self.result[self.curr - 1]) } else { None } } } /// ScAIList Iterator pub struct IterScAIList<'a, T> where T: Clone + Eq + std::fmt::Debug + 'a, { inner: &'a ScAIList<T>, pos: usize, } impl<'a, T: Clone + Eq + std::fmt::Debug> Iterator for IterScAIList<'a, T> { type Item = &'a Interval<T>; fn next(&mut self) -> Option<Self::Item> { if self.pos >= self.inner.intervals.len() { None } else { self.pos += 1; Some(&self.inner.intervals[self.pos - 1]) } } } impl<T: Clone + Eq + std::fmt::Debug> Interval<T> { /// Compute the intersect between two intervals #[inline] pub fn intersect(&self, other: &Self) -> u32 { std::cmp::min(self.end, other.end) .checked_sub(std::cmp::max(self.start, other.start)) .unwrap_or(0) } /// Internal version of intersect for working with IntervalNode / Interval pub fn intersect_raw(&self, start: u32, end: u32) -> u32 { std::cmp::min(self.end, end) .checked_sub(std::cmp::max(self.start, start)) .unwrap_or(0) } /// Check if two intervals overlap #[inline] pub fn overlap(&self, start: u32, end: u32) -> bool { self.start < end && self.end > start } } impl<T: Clone + Eq + std::fmt::Debug> Ord for Interval<T> { #[inline] fn cmp(&self, other: &Self) -> Ordering { if self.start < other.start { Ordering::Less } else if other.start < self.start { Ordering::Greater } else { self.end.cmp(&other.end) } } } impl<T: Clone + Eq + std::fmt::Debug> PartialOrd for Interval<T> { #[inline] fn partial_cmp(&self, other: &Self) -> Option<Ordering> { Some(self.cmp(&other)) } } impl<T: Clone + Eq + std::fmt::Debug> PartialEq for Interval<T> { #[inline] fn eq(&self, other: &Self) -> bool { self.start == other.start && self.end == other.end } } #[cfg(test)] #[rustfmt::skip] mod tests { use super::*; type Iv = Interval<u32>; fn setup_nonoverlapping() -> ScAIList<u32> { let data: Vec<Iv> = (0..100) .step_by(20) .map(|x| Iv { start: x, end: x + 10, val: 0, }) .collect(); let lapper = ScAIList::new(data, None); lapper } fn setup_overlapping() -> ScAIList<u32> { let data: Vec<Iv> = (0..100) .step_by(10) .map(|x| Iv { start: x, end: x + 15, val: 0, }) .collect(); let lapper = ScAIList::new(data, None); lapper } fn setup_badlapper() -> ScAIList<u32> { let data: Vec<Iv> = vec![ Iv{start: 70, end: 120, val: 0}, // max_len = 50 Iv{start: 10, end: 15, val: 0}, Iv{start: 10, end: 15, val: 0}, // exact overlap Iv{start: 12, end: 15, val: 0}, // inner overlap Iv{start: 14, end: 16, val: 0}, // overlap end Iv{start: 40, end: 45, val: 0}, Iv{start: 50, end: 55, val: 0}, Iv{start: 60, end: 65, val: 0}, Iv{start: 68, end: 71, val: 0}, // overlap start Iv{start: 70, end: 75, val: 0}, ]; let lapper = ScAIList::new(data, None); lapper } fn setup_single() -> ScAIList<u32> { let data: Vec<Iv> = vec![Iv { start: 10, end: 35, val: 0, }]; let lapper = ScAIList::new(data, None); lapper } // Test that a query end that hits an interval start returns no interval #[test] fn test_query_end_interval_start() { let lapper = setup_nonoverlapping(); let mut cursor = 0; assert_eq!(None, lapper.find(15, 20).next()); //assert_eq!(None, lapper.seek(15, 20, &mut cursor).next()) } // Test that a query start that hits an interval end returns no interval #[test] fn test_query_start_interval_end() { let lapper = setup_nonoverlapping(); //let mut cursor = 0; assert_eq!(None, lapper.find(30, 35).next()); //assert_eq!(None, lapper.seek(30, 35, &mut cursor).next()) } // Test that a query that overlaps the start of an interval returns that interval #[test] fn test_query_overlaps_interval_start() { let lapper = setup_nonoverlapping(); //let mut cursor = 0; let expected = Iv { start: 20, end: 30, val: 0, }; assert_eq!(Some(&expected), lapper.find(15, 25).next()); //assert_eq!(Some(&expected), lapper.seek(15, 25, &mut cursor).next()) } // Test that a query that overlaps the end of an interval returns that interval #[test] fn test_query_overlaps_interval_end() { let lapper = setup_nonoverlapping(); //let mut cursor = 0; let expected = Iv { start: 20, end: 30, val: 0, }; assert_eq!(Some(&expected), lapper.find(25, 35).next()); //assert_eq!(Some(&expected), lapper.seek(25, 35, &mut cursor).next()) } // Test that a query that is enveloped by interval returns interval #[test] fn test_interval_envelops_query() { let lapper = setup_nonoverlapping(); //let mut cursor = 0; let expected = Iv { start: 20, end: 30, val: 0, }; assert_eq!(Some(&expected), lapper.find(22, 27).next()); //assert_eq!(Some(&expected), lapper.seek(22, 27, &mut cursor).next()) } // Test that a query that envolops an interval returns that interval #[test] fn test_query_envolops_interval() { let lapper = setup_nonoverlapping(); //let mut cursor = 0; let expected = Iv { start: 20, end: 30, val: 0, }; assert_eq!(Some(&expected), lapper.find(15, 35).next()); //assert_eq!(Some(&expected), lapper.seek(15, 35, &mut cursor).next()) } #[test] fn test_overlapping_intervals() { let lapper = setup_overlapping(); //let mut cursor = 0; let e1 = Iv { start: 0, end: 15, val: 0, }; let e2 = Iv { start: 10, end: 25, val: 0, }; assert_eq!(vec![&e1, &e2], lapper.find(8, 20).collect::<Vec<&Iv>>()); //assert_eq!( //vec![&e1, &e2], //lapper.seek(8, 20, &mut cursor).collect::<Vec<&Iv>>() //); } //#[test] //fn test_merge_overlaps() { //let mut lapper = setup_badlapper(); //let expected: Vec<&Iv> = vec![ //&Iv{start: 10, end: 16, val: 0}, //&Iv{start: 40, end: 45, val: 0}, //&Iv{start: 50, end: 55, val: 0}, //&Iv{start: 60, end: 65, val: 0}, //&Iv{start: 68, end: 120, val: 0}, // max_len = 50 //]; //lapper.merge_overlaps(); //assert_eq!(expected, lapper.iter().collect::<Vec<&Iv>>()) //} //#[test] //fn test_lapper_cov() { //let mut lapper = setup_badlapper(); //let before = lapper.cov(); //lapper.merge_overlaps(); //let after = lapper.cov(); //assert_eq!(before, after); //let mut lapper = setup_nonoverlapping(); //lapper.set_cov(); //assert_eq!(lapper.cov(), 50); //} #[test] fn test_interval_intersects() { let i1 = Iv{start: 70, end: 120, val: 0}; // max_len = 50 let i2 = Iv{start: 10, end: 15, val: 0}; let i3 = Iv{start: 10, end: 15, val: 0}; // exact overlap let i4 = Iv{start: 12, end: 15, val: 0}; // inner overlap let i5 = Iv{start: 14, end: 16, val: 0}; // overlap end let i6 = Iv{start: 40, end: 50, val: 0}; let i7 = Iv{start: 50, end: 55, val: 0}; let i_8 = Iv{start: 60, end: 65, val: 0}; let i9 = Iv{start: 68, end: 71, val: 0}; // overlap start let i10 = Iv{start: 70, end: 75, val: 0}; assert_eq!(i2.intersect(&i3), 5); // exact match assert_eq!(i2.intersect(&i4), 3); // inner intersect assert_eq!(i2.intersect(&i5), 1); // end intersect assert_eq!(i9.intersect(&i10), 1); // start intersect assert_eq!(i7.intersect(&i_8), 0); // no intersect assert_eq!(i6.intersect(&i7), 0); // no intersect end = start assert_eq!(i1.intersect(&i10), 5); // inner intersect at start } //#[test] //fn test_union_and_intersect() { //let data1: Vec<Iv> = vec![ //Iv{start: 70, end: 120, val: 0}, // max_len = 50 //Iv{start: 10, end: 15, val: 0}, // exact overlap //Iv{start: 12, end: 15, val: 0}, // inner overlap //Iv{start: 14, end: 16, val: 0}, // overlap end //Iv{start: 68, end: 71, val: 0}, // overlap start //]; //let data2: Vec<Iv> = vec![ //Iv{start: 10, end: 15, val: 0}, //Iv{start: 40, end: 45, val: 0}, //Iv{start: 50, end: 55, val: 0}, //Iv{start: 60, end: 65, val: 0}, //Iv{start: 70, end: 75, val: 0}, //]; //let (mut lapper1, mut lapper2) = (ScAIList::new(data1), ScAIList::new(data2)) ; //// Should be the same either way it's calculated //let (union, intersect) = lapper1.union_and_intersect(&lapper2); //assert_eq!(intersect, 10); //assert_eq!(union, 73); //let (union, intersect) = lapper2.union_and_intersect(&lapper1); //assert_eq!(intersect, 10); //assert_eq!(union, 73); //lapper1.merge_overlaps(); //lapper1.set_cov(); //lapper2.merge_overlaps(); //lapper2.set_cov(); //// Should be the same either way it's calculated //let (union, intersect) = lapper1.union_and_intersect(&lapper2); //assert_eq!(intersect, 10); //assert_eq!(union, 73); //let (union, intersect) = lapper2.union_and_intersect(&lapper1); //assert_eq!(intersect, 10); //assert_eq!(union, 73); //} #[test] fn test_find_overlaps_in_large_intervals() { let data1: Vec<Iv> = vec![ Iv{start: 0, end: 8, val: 0}, Iv{start: 1, end: 10, val: 0}, Iv{start: 2, end: 5, val: 0}, Iv{start: 3, end: 8, val: 0}, Iv{start: 4, end: 7, val: 0}, Iv{start: 5, end: 8, val: 0}, Iv{start: 8, end: 8, val: 0}, Iv{start: 9, end: 11, val: 0}, Iv{start: 10, end: 13, val: 0}, Iv{start: 100, end: 200, val: 0}, Iv{start: 110, end: 120, val: 0}, Iv{start: 110, end: 124, val: 0}, Iv{start: 111, end: 160, val: 0}, Iv{start: 150, end: 200, val: 0}, ]; let lapper = ScAIList::new(data1, None); let found = lapper.find(8, 11).collect::<Vec<&Iv>>(); assert_eq!(found, vec![ &Iv{start: 1, end: 10, val: 0}, &Iv{start: 9, end: 11, val: 0}, &Iv{start: 10, end: 13, val: 0}, ]); let found = lapper.find(145, 151).collect::<Vec<&Iv>>(); assert_eq!(found, vec![ &Iv{start: 100, end: 200, val: 0}, &Iv{start: 111, end: 160, val: 0}, &Iv{start: 150, end: 200, val: 0}, ]); } //#[test] //fn test_depth_sanity() { //let data1: Vec<Iv> = vec![ //Iv{start: 0, end: 10, val: 0}, //Iv{start: 5, end: 10, val: 0} //]; //let lapper = ScAIList::new(data1); //let found = lapper.depth().collect::<Vec<Interval<u32>>>(); //assert_eq!(found, vec![ //Interval{start: 0, end: 5, val: 1}, //Interval{start: 5, end: 10, val: 2} //]); //} //#[test] //fn test_depth_hard() { //let data1: Vec<Iv> = vec![ //Iv{start: 1, end: 10, val: 0}, //Iv{start: 2, end: 5, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 5, end: 8, val: 0}, //Iv{start: 9, end: 11, val: 0}, //]; //let lapper = ScAIList::new(data1); //let found = lapper.depth().collect::<Vec<Interval<u32>>>(); //assert_eq!(found, vec![ //Interval{start: 1, end: 2, val: 1}, //Interval{start: 2, end: 3, val: 2}, //Interval{start: 3, end: 8, val: 5}, //Interval{start: 8, end: 9, val: 1}, //Interval{start: 9, end: 10, val: 2}, //Interval{start: 10, end: 11, val: 1}, //]); //} //#[test] //fn test_depth_harder() { //let data1: Vec<Iv> = vec![ //Iv{start: 1, end: 10, val: 0}, //Iv{start: 2, end: 5, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 3, end: 8, val: 0}, //Iv{start: 5, end: 8, val: 0}, //Iv{start: 9, end: 11, val: 0}, //Iv{start: 15, end: 20, val: 0}, //]; //let lapper = ScAIList::new(data1); //let found = lapper.depth().collect::<Vec<Interval<u32>>>(); //assert_eq!(found, vec![ //Interval{start: 1, end: 2, val: 1}, //Interval{start: 2, end: 3, val: 2}, //Interval{start: 3, end: 8, val: 5}, //Interval{start: 8, end: 9, val: 1}, //Interval{start: 9, end: 10, val: 2}, //Interval{start: 10, end: 11, val: 1}, //Interval{start: 15, end: 20, val: 1}, //]); //} // BUG TESTS - these are tests that came from real life // Test that it's not possible to induce index out of bounds by pushing the cursor past the end // of the lapper. //#[test] //fn test_seek_over_len() { //let lapper = setup_nonoverlapping(); //let single = setup_single(); //let mut cursor: usize = 0; //for interval in lapper.iter() { //for o_interval in single.seek(interval.start, interval.end, &mut cursor) { //println!("{:#?}", o_interval); //} //} //} // Test that if lower_bound puts us before the first match, we still return a match #[test] fn test_find_over_behind_first_match() { let lapper = setup_badlapper(); let e1 = Iv {start: 50, end: 55, val: 0}; let found = lapper.find(50, 55).next(); assert_eq!(found, Some(&e1)); } // When there is a very long interval that spans many little intervals, test that the little // intevals still get returne properly #[test] fn test_bad_skips() { let data = vec![ Iv{start:25264912, end: 25264986, val: 0}, Iv{start:27273024, end: 27273065 , val: 0}, Iv{start:27440273, end: 27440318 , val: 0}, Iv{start:27488033, end: 27488125 , val: 0}, Iv{start:27938410, end: 27938470 , val: 0}, Iv{start:27959118, end: 27959171 , val: 0}, Iv{start:28866309, end: 33141404 , val: 0}, ]; let lapper = ScAIList::new(data, None); let found = lapper.find(28974798, 33141355).collect::<Vec<&Iv>>(); assert_eq!(found, vec![ &Iv{start:28866309, end: 33141404 , val: 0}, ]) } }