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
|
/*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 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 3 of the License, or
* (at your option) any later version.
*
* HISAT 2 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
#include "ds.h"
#include "repeat.h"
#include "rfm.h"
#include "ht2.h"
#include "ht2_handle.h"
EXPORT
void ht2_repeat_dump_repeatmap(ht2_handle_t handle)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
size_t localRFMSize = hp->rgfm->_localRFMs.size();
cerr << "ht2lib: " << "LocalRFM size: " << localRFMSize << endl;
cerr << "ht2lib: " << "Dump repeatMap" << endl;
// repID -> 0
const EList<pair<index_t, index_t> >& repeatMap = hp->repeatdb->repeatMap()[0];
cerr << repeatMap.size() << endl;
for(size_t i = 0; i < repeatMap.size(); i++) {
cerr << repeatMap[i].first << ", " << repeatMap[i].second << endl;
}
}
EXPORT
ht2_error_t ht2_repeat_expand(ht2_handle_t handle,
const char *repeat_name,
uint64_t repeat_pos,
uint64_t repeat_len,
struct ht2_repeat_expand_result **result_ptr)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
index_t rep_id = hp->rgfm->getLocalRFM_idx(repeat_name);
TIndexOffU left = repeat_pos;
TIndexOffU right = left + repeat_len;
bool ret = hp->repeatdb->repeatExist(rep_id, left, right);
if(!ret) {
return HT2_ERR_NOT_REPEAT;
}
/* get coord */
EList<pair<RepeatCoord<index_t>, RepeatCoord<index_t> > > positions;
EList<index_t> snp_id_list;
snp_id_list.clear();
hp->repeatdb->getCoords(
rep_id,
left, right,
snp_id_list,
*(hp->raltdb),
positions
);
/* build result */
size_t result_size = sizeof(struct ht2_repeat_expand_result) + positions.size() * sizeof(struct ht2_position);
struct ht2_repeat_expand_result *result = (struct ht2_repeat_expand_result *)malloc(result_size);
result->count = positions.size();
for(size_t i = 0; i < positions.size(); i++) {
const RepeatCoord<index_t>& coord = positions[i].first;
result->positions[i].chr_id = coord.tid;
result->positions[i].pos = coord.toff;
result->positions[i].direction = coord.fw ? 0 : 1;
}
*(result_ptr) = result;
return HT2_OK;
}
|
