81 lines
2.3 KiB
C++
81 lines
2.3 KiB
C++
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/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <iostream>
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#include "ds.h"
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#include "repeat.h"
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#include "rfm.h"
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#include "ht2.h"
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#include "ht2_handle.h"
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EXPORT
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const char* ht2_index_getrefnamebyid(ht2_handle_t handle, uint32_t chr_id)
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{
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struct ht2_handle *hp = (struct ht2_handle *)handle;
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size_t refname_size = hp->gfm->_refnames.size();
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if(chr_id < (refname_size - 1)) {
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return hp->gfm->_refnames[chr_id].c_str();
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}
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return NULL;
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}
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EXPORT
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ht2_error_t ht2_index_getrefnames(ht2_handle_t handle, struct ht2_index_getrefnames_result **result_ptr)
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{
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struct ht2_handle *hp = (struct ht2_handle *)handle;
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size_t refname_size = hp->gfm->_refnames.size();
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if(refname_size == 0) {
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return HT2_ERR;
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}
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size_t result_hdr_size = sizeof(struct ht2_index_getrefnames_result) + sizeof(char *) * refname_size;
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size_t result_buf_size = 0;
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for(size_t i = 0; i < refname_size - 1; i++) {
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result_buf_size += strlen(hp->gfm->_refnames[i].c_str()) + 1;
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}
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void* ptr = malloc(result_hdr_size + result_buf_size);
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char* buf_ptr = (char *)ptr + result_hdr_size;
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memset(ptr, 0, result_hdr_size + result_buf_size);
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struct ht2_index_getrefnames_result* result = (struct ht2_index_getrefnames_result *)ptr;
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result->count = refname_size - 1;
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result->names[0] = buf_ptr;
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for(size_t i = 0; i < refname_size - 1; i++) {
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size_t rlen = strlen(hp->gfm->_refnames[i].c_str());
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strcpy(result->names[i], hp->gfm->_refnames[i].c_str());
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result->names[i + 1] = result->names[i] + rlen + 1;
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}
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(*result_ptr) = result;
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return HT2_OK;
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}
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