104 lines
2.8 KiB
C++
104 lines
2.8 KiB
C++
/*
|
|
* 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;
|
|
}
|
|
|