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/**
* WHAM - high-throughput sequence aligner
* Copyright (C) 2011 WHAM Group, University of Wisconsin
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
/* $Id: main.cpp 135 2012-03-23 07:47:27Z yinan $ */
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <assert.h>
#include <time.h>
#include <pthread.h>
#ifndef WIN32
#include <sys/time.h>
#endif
#include <unistd.h>
#include <fstream>
#include "error.h"
#include "aligner.h"
#include "rdtsc.h"
#include "util.h"
using namespace std;
char pgversion[] = "0.1.3";
char * pgcommand;
int main(int argc, char* argv[]) {
char basepath[256] = "";
char newpath[256] = "";
srand((unsigned int) time(NULL));
strcpy(basepath, argv[1]);
strcpy(newpath, argv[2]);
if (basepath[0] == '\0') {
elog(ERROR, "specify the base name.\n");
printf("See usage message by specifying -h/--help.\n");
exit(1);
}
if (newpath[0] == '\0') {
elog(ERROR, "specify the new name.\n");
printf("See usage message by specifying -h/--help.\n");
exit(1);
}
elog(INFO, "loading WHAM indexes...\n");
/* load index header */
Aligner * aligner = new Aligner(basepath);
aligner->printInfo();
/* load hash tables */
int ret = aligner->loadHashtables(basepath);
if (ret != SUCCESS) {
elog(ERROR, "failed to load indexes.\n");
}
aligner->sortList();
/*
elog(INFO, "saving indexes...\n");
ret = aligner->saveHead(newpath);
if (ret != SUCCESS) {
elog(ERROR, "failed to save index head.\n");
return ret;
}
ret = aligner->saveIndex(newpath, 0);
if (ret != SUCCESS) {
elog(ERROR, "failed to save index.\n");
return ret;
}
*/
return SUCCESS;
}
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