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// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
// Copyright 2013-2017, Julian Catchen <jcatchen@illinois.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/>.
//
#include "gzFasta.h"
#ifdef HAVE_LIBZ
GzFasta::GzFasta(const char *path) : Input(), gz_fh(NULL)
{
this->open(path);
}
void
GzFasta::open(const char *path)
{
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
int first = gzgetc(gz_fh);
if (first == -1) {
int errnum;
const char* errstr = gzerror(gz_fh, &errnum);
cerr << "Error: Failed to read any content from '" << path
<< "' (gzerror: " << errstr << ").\n";
exit(EXIT_FAILURE);
} else if (first != '>') {
cerr << "Error: '" << path << "': not in fasta format (expected '>', got 0x"
<< std::hex << first << " '" << flush << (char) first << "')."
<< " (note: using zlib version " << zlibVersion()
<< "; compiled with zlib version " << ZLIB_VERSION << ")\n" << flush;
exit(EXIT_FAILURE);
}
gzrewind(gz_fh);
}
Seq *
GzFasta::next_seq()
{
#ifdef DEBUG
DOES_NOT_HAPPEN; // As this function isn't efficient.
#endif
Seq* s = new Seq();
s->id = new char[id_len];
if(!next_seq(*s)) {
delete s;
return NULL;
}
return s;
}
int
GzFasta::next_seq(Seq &s)
{
this->buf.clear();
//
// Check the contents of the line buffer. When we finish reading a FASTA record
// the buffer will either contain whitespace or the header of the next FAST
// record.
//
while (this->line[0] != '>' && !gzeof(this->gz_fh)) {
gzgets(this->gz_fh, this->line, max_len);
}
if (gzeof(this->gz_fh)) {
return false;
}
//
// Check if there is a carraige return in the buffer
//
uint len = strlen(this->line);
if (len >= 1 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len >= 2 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
//
// Check if the ID line of the FASTA file has a comment after the ID.
//
char* q = this->line + 1;
++q;
while (*q != '\0' && *q != ' ' && *q != '\t')
++q;
if (*q != '\0') {
// Comment present.
*q = '\0';
++q;
s.comment.assign(q);
}
assert(s.id != NULL);
strcpy(s.id, this->line + 1);
//
// Read the sequence from the file -- keep reading lines until we reach the next
// record or the end of file.
//
gzgets(this->gz_fh, this->line, max_len);
while (this->line[0] != '>' && !gzeof(this->gz_fh)) {
len = strlen(this->line);
if (len >= 1 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len >= 2 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
this->buf += this->line;
this->line[0] = '\0';
gzgets(this->gz_fh, this->line, max_len);
}
if (gzeof(this->gz_fh)) {
len = strlen(this->line);
if (len >= 1 && this->line[len - 1] == '\n') this->line[len - 1] = '\0';
if (len >= 2 && this->line[len - 2] == '\r') this->line[len - 2] = '\0';
this->buf += this->line;
this->line[0] = '\0';
}
s.reserve(buf.length(), false);
strcpy(s.seq, this->buf.c_str());
return true;
}
#endif // HAVE_LIBZ
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