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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"
using namespace std;
MemoryTally gMemTally;
static const struct ht2_options ht2_default_options = {
.offRate = -1,
.useMm = false,
.useShmem = false,
.mmSweep = false,
.noRefNames = false,
.noSplicedAlignment = false,
.gVerbose = false,
.startVerbose = false,
.sanityCheck = 0,
.useHaplotype = false,
};
static void free_handle(struct ht2_handle *hp)
{
if(hp->altdb) {
delete hp->altdb;
}
if(hp->raltdb) {
delete hp->raltdb;
}
if(hp->repeatdb) {
delete hp->repeatdb;
}
if(hp->gfm) {
if(hp->gfm->isInMemory()) {
hp->gfm->evictFromMemory();
}
delete hp->gfm;
}
if(hp->rgfm) {
if(hp->rgfm->isInMemory()) {
hp->rgfm->evictFromMemory();
}
delete hp->rgfm;
}
delete hp;
}
static void init_handle(struct ht2_handle *hp)
{
struct ht2_options *opt = &hp->options;
hp->altdb = new ALTDB<index_t>();
hp->repeatdb = new RepeatDB<TIndexOffU>();
hp->raltdb = new ALTDB<index_t>();
hp->gfm = new HGFM<TIndexOffU, local_index_t>(
hp->ht2_idx_name,
hp->altdb,
NULL,
NULL,
-1,
true,
opt->offRate,
0,
opt->useMm,
opt->useShmem,
opt->mmSweep,
!opt->noRefNames,
true,
true,
true,
!opt->noSplicedAlignment,
opt->gVerbose,
opt->startVerbose,
false,
opt->sanityCheck,
opt->useHaplotype);
// Load the other half of the index into memory
assert(!hp->gfm->isInMemory());
hp->gfm->loadIntoMemory(
-1,
true,
true,
true,
!opt->noRefNames,
opt->startVerbose);
hp->rgfm = new RFM<TIndexOffU>(
hp->ht2_idx_name + ".rep",
hp->raltdb,
hp->repeatdb,
NULL,
-1,
true,
opt->offRate,
0,
opt->useMm,
opt->useShmem,
opt->mmSweep,
!opt->noRefNames,
true,
true,
true,
!opt->noSplicedAlignment,
opt->gVerbose,
opt->startVerbose,
false,
opt->sanityCheck,
false);
assert(!hp->rgfm->isInMemory());
hp->rgfm->loadIntoMemory(
-1,
true,
true,
true,
!opt->noRefNames,
opt->startVerbose);
hp->repeatdb->construct(hp->gfm->rstarts(), hp->gfm->nFrag());
}
EXPORT
ht2_handle_t ht2_init(const char *name, ht2_option_t *options)
{
struct ht2_handle *handle = new ht2_handle;
handle->ht2_idx_name = name;
if(options) {
memcpy(&handle->options, options, sizeof(struct ht2_options));
} else {
memcpy(&handle->options, &ht2_default_options, sizeof(struct ht2_options));
}
// Init
init_handle(handle);
handle->tmp_str = name;
return (ht2_handle_t)handle;
}
EXPORT
void ht2_close(ht2_handle_t handle)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
if(hp == NULL) {
return;
}
free_handle(hp);
}
EXPORT
ht2_error_t ht2_init_options(ht2_option_t *options)
{
if(options == NULL) {
return HT2_ERR;
}
memcpy(options, &ht2_default_options, sizeof(ht2_default_options));
return HT2_OK;
}
EXPORT
void ht2_test_1(ht2_handle_t handle)
{
struct ht2_handle *hp = (struct ht2_handle *)handle;
size_t refname_size = hp->gfm->_refnames.size();
cerr << "ht2lib: " << "gfm refnames: " << refname_size << endl;
for(size_t i = 0; i < refname_size; i++) {
cerr << "ht2lib: " << " " << i << " -> " << hp->gfm->_refnames[i] << endl;
}
}
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