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/*
* 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
const char* ht2_index_getrefnamebyid(ht2_handle_t handle, uint32_t chr_id)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
size_t refname_size = hp->gfm->_refnames.size();
if(chr_id < (refname_size - 1)) {
return hp->gfm->_refnames[chr_id].c_str();
}
return NULL;
}
EXPORT
ht2_error_t ht2_index_getrefnames(ht2_handle_t handle, struct ht2_index_getrefnames_result **result_ptr)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
size_t refname_size = hp->gfm->_refnames.size();
if(refname_size == 0) {
return HT2_ERR;
}
size_t result_hdr_size = sizeof(struct ht2_index_getrefnames_result) + sizeof(char *) * refname_size;
size_t result_buf_size = 0;
for(size_t i = 0; i < refname_size - 1; i++) {
result_buf_size += strlen(hp->gfm->_refnames[i].c_str()) + 1;
}
void* ptr = malloc(result_hdr_size + result_buf_size);
char* buf_ptr = (char *)ptr + result_hdr_size;
memset(ptr, 0, result_hdr_size + result_buf_size);
struct ht2_index_getrefnames_result* result = (struct ht2_index_getrefnames_result *)ptr;
result->count = refname_size - 1;
result->names[0] = buf_ptr;
for(size_t i = 0; i < refname_size - 1; i++) {
size_t rlen = strlen(hp->gfm->_refnames[i].c_str());
strcpy(result->names[i], hp->gfm->_refnames[i].c_str());
result->names[i + 1] = result->names[i] + rlen + 1;
}
(*result_ptr) = result;
return HT2_OK;
}
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