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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 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.
*
* Bowtie 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
#include <fstream>
#include <string.h>
#include <stdlib.h>
#include "tokenize.h"
#include "ds.h"
#ifdef ENABLE_x86_64_v3
#include <unistd.h>
#endif
using namespace std;
extern "C" {
int bowtie(int argc, const char **argv);
}
#ifdef ENABLE_x86_64_v3
void check_x86_64_v3(int argc, const char **argv) {
if (__builtin_cpu_supports ("x86-64-v3") && (argc<126)) {
const char* new_argv[128]; // should always be enough, but above check enforces it, too
const char * org_path = argv[0];
// Append -v256 to the original path
const int fn_len = strlen(org_path);
char *new_path = (char*) malloc(fn_len+16);
memcpy(new_path,org_path,fn_len);
strncpy(new_path+fn_len,"-v256",15);
for (int i=1; i<=argc; i++) new_argv[i] = argv[i]; // all but first the same, also copy final NULL
new_argv[0] = new_path;
// now replace the executable with new variant
// assuming the executable exists... execvp will gracefully fail else, which is OK
execvp(new_argv[0], (char *const *)new_argv);
// we should never get out of the above call
fprintf(stderr,"[WARNING] Failed to launch x86-64-v3 version, staying with default\n");
}
}
#endif
/**
* Bowtie main function. It is placed in a separate source file to
* make it slightly easier to compile Bowtie as a library.
*
* If the user specifies -A <file> as the first two arguments, main
* will interpret that file as having one set of command-line arguments
* per line, and will dispatch each batch of arguments one at a time to
* bowtie.
*/
int main(int argc, const char **argv) {
#ifdef ENABLE_x86_64_v3
check_x86_64_v3(argc, argv);
#endif
if(argc > 2 && strcmp(argv[1], "-A") == 0) {
const char *file = argv[2];
ifstream in;
in.open(file);
char buf[4096];
int lastret = -1;
while(in.getline(buf, 4095)) {
EList<string> args;
args.push_back(string(argv[0]));
tokenize(buf, " \t", args);
const char **myargs = (const char**)malloc(sizeof(char*)*args.size());
for(size_t i = 0; i < args.size(); i++) {
myargs[i] = args[i].c_str();
}
if(args.size() == 1) continue;
lastret = bowtie((int)args.size(), myargs);
free(myargs);
}
if(lastret == -1) {
cerr << "Warning: No arg strings parsed from " << file << endl;
return 0;
}
return lastret;
} else {
return bowtie(argc, argv);
}
}
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