1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
use crate::{
traits::{IntervalBounds, ValueBounds},
Container,
};
/// Identifies the lower bound on a [Conitainer] via a binary tree search
pub trait Bound<T, I>: Container<T, I>
where
I: IntervalBounds<T>,
T: ValueBounds,
{
/// Identifies the lower bound on the [Container] via a binary tree search
/// for a provided query.
///
/// This first checks if the [Container] is sorted
///
/// ## On base coordinates
///
/// ```
/// use bedrs::{Bound, Container, Interval, IntervalSet};
///
/// let records = vec![
/// Interval::new(10, 20),
/// Interval::new(20, 30), // <- min
/// Interval::new(30, 40),
/// Interval::new(40, 50),
/// Interval::new(50, 60),
/// ];
/// let query = Interval::new(17, 27);
/// let mut set = IntervalSet::new(records);
/// set.sort();
/// let bound = set.lower_bound(&query);
/// assert_eq!(bound, Some(1));
/// ```
///
/// ## On genomic coordinates
///
/// ```
/// use bedrs::{Bound, Container, GenomicInterval, GenomicIntervalSet};
///
/// let records = vec![
/// GenomicInterval::new(1, 10, 20),
/// GenomicInterval::new(2, 10, 20),
/// GenomicInterval::new(3, 10, 20), // <- min
/// GenomicInterval::new(3, 20, 20),
/// GenomicInterval::new(3, 30, 20),
/// GenomicInterval::new(4, 10, 20),
/// ];
/// let mut set = GenomicIntervalSet::new(records);
/// set.sort();
/// let query = GenomicInterval::new(3, 10, 20);
/// let bound = set.lower_bound(&query);
/// assert_eq!(bound, Some(2));
/// ```
fn lower_bound(&self, query: &I) -> Option<usize> {
if self.is_sorted() {
Some(self.lower_bound_unchecked(query))
} else {
None
}
}
/// Identifies the lower bound on the [Container] via a binary tree search
/// for a provided query.
///
/// Does not perform a check if it is sorted beforehand.
/// Use at your own risk.
///
/// ## On base coordinates
///
/// ```
/// use bedrs::{Bound, Interval, IntervalSet};
///
/// let records = vec![
/// Interval::new(10, 20),
/// Interval::new(20, 30), // <- min
/// Interval::new(30, 40),
/// Interval::new(40, 50),
/// Interval::new(50, 60),
/// ];
/// let query = Interval::new(17, 27);
/// let set = IntervalSet::new(records);
/// let bound = set.lower_bound_unchecked(&query);
/// assert_eq!(bound, 1);
/// ```
///
/// ## On genomic coordinates
///
/// ```
/// use bedrs::{Bound, GenomicInterval, GenomicIntervalSet};
///
/// let records = vec![
/// GenomicInterval::new(1, 10, 20),
/// GenomicInterval::new(2, 10, 20),
/// GenomicInterval::new(3, 10, 20), // <- min
/// GenomicInterval::new(3, 20, 20),
/// GenomicInterval::new(3, 30, 20),
/// GenomicInterval::new(4, 10, 20),
/// ];
/// let set = GenomicIntervalSet::new(records);
/// let query = GenomicInterval::new(3, 10, 20);
/// let bound = set.lower_bound_unchecked(&query);
/// assert_eq!(bound, 2);
/// ```
fn lower_bound_unchecked(&self, query: &I) -> usize {
let mut high = self.len();
let mut low = 0;
while high > 0 {
let mid = high / 2;
let top_half = high - mid;
let low_index = low + mid;
let top_index = low + top_half;
let test_interval = &self.records()[low_index];
high = mid;
low = if test_interval.lt(query) {
top_index
} else {
low
};
}
low
}
}
#[cfg(test)]
mod testing {
use crate::{Bound, Container, GenomicInterval, GenomicIntervalSet, Interval, IntervalSet};
#[test]
fn bsearch_base_low() {
let records = (0..500).map(|x| Interval::new(x, x + 50)).collect();
let mut set = IntervalSet::new(records);
set.sort();
let query = Interval::new(10, 20);
let bound = set.lower_bound(&query);
assert_eq!(bound, Some(10));
}
#[test]
fn bsearch_base_high() {
let records = (0..500).map(|x| Interval::new(x, x + 50)).collect();
let mut set = IntervalSet::new(records);
set.sort();
let query = Interval::new(300, 320);
let bound = set.lower_bound(&query);
assert_eq!(bound, Some(300));
}
#[test]
fn bsearch_genomic_low() {
let records = vec![
GenomicInterval::new(1, 10, 20),
GenomicInterval::new(2, 10, 20),
GenomicInterval::new(3, 10, 20), // <- min
GenomicInterval::new(3, 20, 20),
GenomicInterval::new(3, 30, 20),
GenomicInterval::new(4, 10, 20),
];
let mut set = GenomicIntervalSet::new(records);
set.sort();
let query = GenomicInterval::new(3, 10, 20);
let bound = set.lower_bound(&query);
assert_eq!(bound, Some(2));
}
#[test]
fn bsearch_genomic_high() {
let records = vec![
GenomicInterval::new(1, 10, 20),
GenomicInterval::new(2, 10, 20),
GenomicInterval::new(3, 10, 20),
GenomicInterval::new(3, 20, 20),
GenomicInterval::new(3, 30, 20), // <- min
GenomicInterval::new(4, 10, 20),
];
let mut set = GenomicIntervalSet::new(records);
set.sort();
let query = GenomicInterval::new(3, 25, 20);
let bound = set.lower_bound(&query);
assert_eq!(bound, Some(4));
}
#[test]
fn bsearch_unsorted() {
let records = (0..500).map(|x| Interval::new(x, x + 50)).collect();
let set = IntervalSet::new(records);
let query = Interval::new(10, 20);
let bound = set.lower_bound(&query);
assert!(bound.is_none());
}
#[test]
fn bsearch_equality() {
let records = vec![
Interval::new(10, 20),
Interval::new(20, 30), // <- min
Interval::new(30, 40),
Interval::new(40, 50),
Interval::new(50, 60),
];
let query = Interval::new(20, 25);
let set = IntervalSet::new(records);
let bound = set.lower_bound_unchecked(&query);
assert_eq!(bound, 1);
}
}