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
|
/*
This file is part of Sambamba.
Copyright (C) 2017 Pjotr Prins <pjotr.prins@thebird.nl>
Sambamba is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.
Sambamba is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
02111-1307 USA
*/
module bio.std.experimental.hts.reads;
import bio.std.experimental.hts.constants;
import bio.core.utils.exception;
import std.stdio;
bool read_overlaps(R)(GenomeLocation loc, R r) {
assert(r.is_mapped);
return r.ref_id == loc.ref_id && loc.pos >= r.start_pos && loc.pos <= r.end_pos;
}
bool reads_overlap(R)(R r1, R r2) {
asserte(r1.is_mapped);
asserte(r2.is_mapped);
asserte(r2.ref_id == r1.ref_id);
// r1 rrrrrrrrrrr
// r2 ---------???????????
if (r2.start_pos < r1.start_pos && r2.end_pos >= r1.start_pos) {
return true;
}
// r1 rrrrrrrrrrr
// r2 ----?????
return r2.start_pos >= r1.start_pos && r2.start_pos <= r1.end_pos;
}
|
