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// Copyright (C) 2023 Damien Zammit <damien@zamaudio.com>
// Copyright (C) 2010 Herman Stehouwer
//
// 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/>.
#include <sstream>
#include <iostream>
#include <string>
#include "suffixarray.h"
#include "fastastring.h"
#include <vector>
#include <fstream>
#include <cstdlib>
#include <limits>
#define HAVE_GETOPT_H
#ifdef HAVE_GETOPT_H
#define GNU_SOURCE
#include <getopt.h>
#else
extern "C" {
char* optarg;
extern int optind, opterr, optopt;
struct option { const char *name; int has_arg; int *flag; int val; };
#define no_argument 0
#define required_argument 1
#define optional_argument 2
#ifdef HAVE_GETOPT_LONG_ONLY
extern int getopt_long_only (int argc, char * const argv[],
const char *optstring, const struct option *longopts, int
*longindex);
#else
#warning \
Gnu Getopt Library not found: \
cannot implement long option handling
extern int getopt(int argc, char* const argv[], const char*
optstring);
inline int getopt_long_only(int argc, char * const argv[], const char
*optstring, const struct option *longopts, int *longindex) {
return getopt(argc, argv, optstring);
}
#endif
} // extern "C"
#endif // HAVE_GETOPT_H
static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"ref", required_argument, 0, 'r'},
{"query", required_argument, 0, 'q'},
{0, 0, 0, 0}
};
using namespace std;
using namespace ns_suffixarray;
typedef suffixarray<fastastring> sa_fasta;
string program_name;
void usage()
{
cerr << "ruffsort -r (reference fasta) -q (query fastq to split by chr)" << endl;
exit(0);
}
int
main(int argc, char* argv[]) {
program_name = argv[0];
ifstream is, iq;
string refseq;
string refseqsa;
// Handle arguments
int opt;
int option_index;
const char* optstring="hr:q:";
while ((opt = getopt_long_only(argc, argv, optstring, long_options,
&option_index)) !=-1){
switch (opt) {
case 'h':
usage();
break;
case 'r':
refseq = string(optarg);
refseqsa = refseq + string(".sa");
is.open (refseqsa.c_str(), ios::in);
if (!is.good()) {
cerr << "reference has no suffix array generated, indexing now" << endl;
is.open (refseq.c_str(), ios::in);
if (!is.good()) {
cerr << "cannot open input file " << optarg << endl;
exit (-1);
}
fastastring seqs;
is >> seqs;
seqs.push_back('~');
sa_fasta tree(seqs);
is.close();
tree.savesarray(refseqsa);
cout << "Suffix array generated" << endl;
}
is.close();
break;
case 'q':
iq.open (optarg, ios::in);
if (!iq.good()) {
cerr << "query fastq missing" << endl;
exit (-1);
}
break;
default:
cerr << "unknown argument " << opt << endl;
exit (-1);
break;
}
}
is.open (refseq.c_str(), ios::in);
if (!is.good()) {
cerr << "cannot open ref file" << endl;
exit (-1);
}
cerr << "Loading reference sequence" << endl;
fastastring ref;
is >> ref;
ref.push_back('~');
cerr << "Loading suffix array" << endl;
sa_fasta tree(refseqsa, ref);
sa_fasta::size_type result;
fastastring totest;
iq >> totest;
try {
result = tree.find_position(totest, 'N');
} catch (StringNotFound) {
cerr << "Not found" << endl;
exit (0);
}
cout << result << endl;
}
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