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// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
// Copyright 2013, Julian Catchen <jcatchen@uoregon.edu>
//
// This file is part of Stacks.
//
// Stacks 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.
//
// Stacks 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 Stacks. If not, see <http://www.gnu.org/licenses/>.
//
#ifndef __GZFASTQ_H__
#define __GZFASTQ_H__
#ifdef HAVE_LIBZ
#include <cerrno>
#include <zlib.h>
#include "input.h"
class GzFastq: public Input {
gzFile gz_fh;
public:
GzFastq(string path) : Input() {
this->gz_fh = gzopen(path.c_str(), "rb");
if (!this->gz_fh) {
cerr << "Failed to open gzipped file '" << path << "': " << strerror(errno) << ".\n";
exit(EXIT_FAILURE);
}
#if ZLIB_VERNUM >= 0x1240
gzbuffer(this->gz_fh, libz_buffer_size);
#endif
};
GzFastq(const char *path) : Input() {
this->gz_fh = gzopen(path, "rb");
if (!this->gz_fh) {
cerr << "Failed to open gzipped file '" << path << "': " << strerror(errno) << ".\n";
exit(EXIT_FAILURE);
}
#if ZLIB_VERNUM >= 0x1240
gzbuffer(this->gz_fh, libz_buffer_size);
#endif
};
~GzFastq() {
gzclose(this->gz_fh);
};
Seq *next_seq();
int next_seq(Seq &s);
};
Seq *GzFastq::next_seq() {
char *res = NULL;
//
// Check the contents of the line buffer. When we finish reading a FASTQ record
// the buffer will either contain whitespace or the header of the next FASTQ
// record.
//
this->line[0] = '\0';
do {
res = gzgets(this->gz_fh, this->line, max_len);
} while (this->line[0] != '@' && res != NULL);
if (res == NULL) {
return NULL;
}
//
// Check if there is a carraige return in the buffer
//
uint len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
//
// Initialize the Seq structure and store the FASTQ ID
//
Seq *s = new Seq;
s->id = new char[strlen(this->line) + 1];
strcpy(s->id, this->line + 1);
//
// Read the sequence from the file
//
gzgets(this->gz_fh, this->line, max_len);
if (gzeof(this->gz_fh)) {
return NULL;
}
len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
s->seq = new char[len + 1];
strcpy(s->seq, this->line);
//
// Read the repeat of the ID
//
this->line[0] = '\0';
res = gzgets(this->gz_fh, this->line, max_len);
if (this->line[0] != '+' || res == NULL) {
return NULL;
}
//
// Read the quality score from the file
//
this->line[0] = '\0';
res = gzgets(this->gz_fh, this->line, max_len);
if (res == NULL && strlen(this->line) == 0) {
return NULL;
}
len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
s->qual = new char[len + 1];
strcpy(s->qual, this->line);
//
// Clear the line buffer so it is set up for the next record. If a '@'
// appears in the quality scores read, it will break parsing next time
// it is called.
//
this->line[0] = '\0';
return s;
}
int GzFastq::next_seq(Seq &s) {
char *res = NULL;
//
// Check the contents of the line buffer. When we finish reading a FASTQ record
// the buffer will either contain whitespace or the header of the next FASTQ
// record.
//
this->line[0] = '\0';
do {
res = gzgets(this->gz_fh, this->line, max_len);
} while (this->line[0] != '@' && res != NULL);
if (res == NULL) {
return 0;
}
//
// Check if there is a carraige return in the buffer
//
uint len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
//
// Store the FASTQ ID
//
strcpy(s.id, this->line + 1);
//
// Read the sequence from the file
//
this->line[0] = '\0';
res = gzgets(this->gz_fh, this->line, max_len);
if (res == NULL) {
return 0;
}
len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
strcpy(s.seq, this->line);
//
// Read the repeat of the ID
//
this->line[0] = '\0';
res = gzgets(this->gz_fh, this->line, max_len);
if (this->line[0] != '+' || res == NULL) {
return 0;
}
//
// Read the quality score from the file
//
this->line[0] = '\0';
res = gzgets(this->gz_fh, this->line, max_len);
if (res == NULL && strlen(this->line) == 0) {
return 0;
}
len = strlen(this->line);
if (len > 0 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len > 1 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
strcpy(s.qual, this->line);
//
// Clear the line buffer so it is set up for the next record. If a '@'
// appears in the quality scores read, it will break parsing next time
// it is called.
//
this->line[0] = '\0';
return 1;
}
#else // If HAVE_LIBZ is undefined and zlib library is not present.
#include "input.h"
class GzFastq: public Input {
public:
GzFastq(const char *path) : Input() { cerr << "Gzip support was not enabled when Stacks was compiled.\n"; };
GzFastq(string path) : Input() { cerr << "Gzip support was not enabled when Stacks was compiled.\n"; };
~GzFastq() {};
Seq *next_seq() { return NULL; };
int next_seq(Seq &) { return 0; };
};
#endif // HAVE_LIBZ
#endif // __GZFASTQ_H__
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