70 lines
2.0 KiB
C++
70 lines
2.0 KiB
C++
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/*
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* Copyright 2015, 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <iostream>
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#include <fstream>
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#include <string.h>
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#include <stdlib.h>
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#include "tokenize.h"
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#include "ds.h"
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using namespace std;
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extern "C" {
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int hisat2(int argc, const char **argv);
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}
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/**
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* Bowtie main function. It is placed in a separate source file to
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* make it slightly easier to compile Bowtie as a library.
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*
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* If the user specifies -A <file> as the first two arguments, main
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* will interpret that file as having one set of command-line arguments
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* per line, and will dispatch each batch of arguments one at a time to
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* bowtie.
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*/
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int main(int argc, const char **argv) {
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if(argc > 2 && strcmp(argv[1], "-A") == 0) {
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const char *file = argv[2];
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ifstream in;
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in.open(file);
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char buf[4096];
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int lastret = -1;
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while(in.getline(buf, 4095)) {
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EList<string> args;
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args.push_back(string(argv[0]));
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tokenize(buf, " \t", args);
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const char **myargs = (const char**)malloc(sizeof(char*)*args.size());
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for(size_t i = 0; i < args.size(); i++) {
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myargs[i] = args[i].c_str();
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}
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if(args.size() == 1) continue;
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lastret = hisat2((int)args.size(), myargs);
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free(myargs);
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}
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if(lastret == -1) {
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cerr << "Warning: No arg strings parsed from " << file << endl;
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return 0;
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}
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return lastret;
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} else {
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return hisat2(argc, argv);
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}
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}
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