BgzfFileType.cpp
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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/>.
*/
#ifdef __ZLIB_AVAILABLE__
#include <iostream>
#include <string.h>
#include "BgzfFileType.h"
// Default to require the EOF block at the end of the file.
bool BgzfFileType::ourRequireEofBlock = true;
BgzfFileType::BgzfFileType(const char * filename, const char * mode)
{
// If the file is for write and is '-', then write to stdout.
if(((mode[0] == 'w') || (mode[0] == 'W')) &&
(strcmp(filename, "-") == 0))
{
// Write to stdout.
bgzfHandle = bgzf_dopen(fileno(stdout), mode);
}
else if(((mode[0] == 'r') || (mode[0] == 'R')) &&
(strcmp(filename, "-") == 0))
{
// read from stdin
bgzfHandle = bgzf_dopen(fileno(stdin), mode);
}
else
{
bgzfHandle = bgzf_open(filename, mode);
}
myStartPos = 0;
if (bgzfHandle != NULL)
{
// Check to see if the file is being opened for read, if the eof block
// is required, and if it is, if it is there.
if ((mode[0] == 'r' || mode[0] == 'R') && (strcmp(filename, "-") != 0)
&& ourRequireEofBlock && (bgzf_check_EOF(bgzfHandle) != 1))
{
std::cerr << "BGZF EOF marker is missing in " << filename << std::endl;
// the block is supposed to be there, but isn't, so close the file.
close();
}
else
{
// Successfully opened a properly formatted file, so get the start
// position.
myStartPos = bgzf_tell(bgzfHandle);
}
}
myEOF = false;
}
// Set whether or not to require the EOF block at the end of the
// file. True - require the block. False - do not require the block.
void BgzfFileType::setRequireEofBlock(bool requireEofBlock)
{
ourRequireEofBlock = requireEofBlock;
}
#endif