InputFile.h File Reference

#include <stdio.h>
#include <iostream>
#include <cstring>
#include <stdint.h>
#include "FileType.h"

Include dependency graph for InputFile.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
class	InputFile
	Class for easily reading/writing files without having to worry about file type (uncompressed, gzip, bgzf) when reading. More...

Typedefs
typedef InputFile *	IFILE
	Define IFILE as a pointer to an InputFile object.

Functions
IFILE	ifopen (const char *filename, const char *mode, InputFile::ifileCompression compressionMode=InputFile::DEFAULT)
	Open a file with the specified name and mode, using a filename of "-" to indicate stdin/stdout.
int	ifclose (IFILE &file)
	Close the file.
unsigned int	ifread (IFILE file, void *buffer, unsigned int size)
	Read up to size bytes from the file into the buffer.
int	ifgetc (IFILE file)
	Get a character from the file.
bool	ifgetline (IFILE file, void *buffer, size_t max)
	Get a line from the file.
void	ifrewind (IFILE file)
	Reset to the beginning of the file (cannot be done for stdin/stdout).
int	ifeof (IFILE file)
	Check to see if we have reached the EOF (returns 0 if not EOF).
unsigned int	ifwrite (IFILE file, const void *buffer, unsigned int size)
	Write the specified number of bytes from the specified buffer into the file.
int64_t	iftell (IFILE file)
	Get current position in the file.
bool	ifseek (IFILE file, int64_t offset, int origin)
	Seek to the specified position (result from an iftell), but cannot be done for stdin/stdout.
int	ifprintf (IFILE output, const char *format,...)
	Write to a file using fprintf format.
IFILE	operator>> (IFILE stream, std::string &str)
	Read a line from a file using streaming.
InputFile &	operator<< (InputFile &stream, const std::string &str)
	Write to a file using streaming.
InputFile &	operator<< (InputFile &stream, const char *str)
	Write to a file using streaming.
InputFile &	operator<< (InputFile &stream, double num)
	Write to a file using streaming.
InputFile &	operator<< (InputFile &stream, int num)
	Write to a file using streaming.
InputFile &	operator<< (InputFile &stream, unsigned int num)
	Write to a file using streaming.
InputFile &	operator<< (InputFile &stream, char ch)
	Write to a file using streaming.

Typedef Documentation

IFILE

typedef InputFile* IFILE

Define IFILE as a pointer to an InputFile object.

Definition at line 551 of file InputFile.h.

Function Documentation

ifclose()

int ifclose ( IFILE & file )

inline

Close the file.

Parameters

file	file to be closed - IFILE is a pointer to an InputFile object

Returns

status of the close (0 is success or if NULL is passed in).

Definition at line 580 of file InputFile.h.

{
    if(file == NULL)
    {
        // NULL Pointer passed in, so return 0, since no file is open, so
        // does not need to be closed.
        return(0);
    }
    int result = file->ifclose();
    delete file;
    file = NULL;
    return(result);
}

References InputFile::ifclose().

Referenced by FastQFile::closeFile(), GenomeSequence::loadDBSNP(), BamIndex::readIndex(), and SamFile::resetFile().

ifeof()

int ifeof ( IFILE file )

inline

Check to see if we have reached the EOF (returns 0 if not EOF).

Parameters

file	file to be checked - IFILE is a pointer to an InputFile object

Returns

0 if not EOF, any other value means EOF.

Definition at line 654 of file InputFile.h.

{
    if(file == NULL)
    {
        // No file, so that is considered to be EOF, so return 1.
        return(1);
    }
    return(file->ifeof());
}

References InputFile::ifeof().

Referenced by GlfFile::isEOF(), FastQFile::isEof(), GlfRefSection::read(), FastQFile::readFastQSequence(), and SamRecord::setBufferFromFile().

ifgetc()

int ifgetc ( IFILE file )

inline

Get a character from the file.

Read a character from the internal buffer, or if the end of the buffer has been reached, read from the file into the buffer and return index 0.

Parameters

file	file to be read - IFILE is a pointer to an InputFile object

Returns

character that was read or EOF.

Definition at line 615 of file InputFile.h.

{
    if(file == NULL)
    {
        // return eof since there is no file.
        return(EOF);
    }
    return(file->ifgetc());
}

References InputFile::ifgetc().

ifgetline()

bool ifgetline ( IFILE file, void * buffer, size_t max )

inline

Get a line from the file.

Parameters

file	file to be read - IFILE is a pointer to an InputFile object
buffer	the buffer into which data is to be placed
max	the maximum size of the buffer, in bytes

Returns

true if the last character read was an EOF

Definition at line 630 of file InputFile.h.

{
    if(file == NULL)
    {
        // return eof since there is no file.
        return(true);
    }
    return(file->ifgetline(buffer, max));
}

References InputFile::ifgetline().

ifopen()

IFILE ifopen ( const char * filename, const char * mode, InputFile::ifileCompression compressionMode = InputFile::DEFAULT )

inline

Open a file with the specified name and mode, using a filename of "-" to indicate stdin/stdout.

Parameters

filename	file to open ("-" meands stdin/stdout)
mode	same format as fopen: "r" for read & "w" for write.
compressionMode	set the type of file to open for writing or for reading from stdin (when reading files not from stdin, the compression type is determined by reading the file).

Returns

IFILE - pointer to the InputFile object that has been opened.

Definition at line 562 of file InputFile.h.

{
    IFILE file = new InputFile(filename, mode, compressionMode);
    if (!file->isOpen())
    {
 
        // Not open, so delete the file, and return null.
        delete file;
        file = NULL;
    }
    return file;
}

References InputFile::DEFAULT, and InputFile::isOpen().

Referenced by GenomeSequence::loadDBSNP(), FastQFile::openFile(), SamFile::OpenForRead(), GlfFile::openForRead(), SamFile::OpenForWrite(), GlfFile::openForWrite(), BamIndex::readIndex(), and Tabix::readIndex().

ifprintf()

int ifprintf	(	IFILE	output,
		const char *	format,
			... )

Write to a file using fprintf format.

Parameters

file	file to write to - IFILE is a pointer to an InputFile object
format	printf format for writing, followed by parameters.

Returns

number of bytes written

Definition at line 398 of file InputFile.cpp.

{
    String buffer;
 
    va_list  ap;
    va_start(ap, format);
 
    buffer.vprintf(format, ap);
 
    va_end(ap);
 
    return ::ifwrite(output, (const char *) buffer, buffer.Length());
}

ifread()

unsigned int ifread ( IFILE file, void * buffer, unsigned int size )

inline

Read up to size bytes from the file into the buffer.

Parameters

file	file to be read - IFILE is a pointer to an InputFile object
buffer	pointer to memory at least size bytes big to write the data into.
size	number of bytes to be read

Returns

number of bytes read

Definition at line 600 of file InputFile.h.

{
    if(file == NULL)
    {
        // No file was passed in, so 0 bytes were read.
        return(0);
    }
    return(file->ifread(buffer, size));
}

References InputFile::ifread().

Referenced by SamFile::OpenForRead(), GlfHeader::read(), GlfRecord::read(), GlfRefSection::read(), BamIndex::readIndex(), Tabix::readIndex(), and SamRecord::setBufferFromFile().

ifrewind()

void ifrewind ( IFILE file )

inline

Reset to the beginning of the file (cannot be done for stdin/stdout).

Parameters

file	file to be rewound - IFILE is a pointer to an InputFile object

Definition at line 642 of file InputFile.h.

{
    if(file == NULL)
    {
        return;
    }
    file->ifrewind();
}

References InputFile::ifrewind().

Referenced by SamFile::OpenForRead().

ifseek()

bool ifseek ( IFILE file, int64_t offset, int origin )

inline

Seek to the specified position (result from an iftell), but cannot be done for stdin/stdout.

Parameters

file	file to perform seek on - IFILE is a pointer to an InputFile object
offset	offset into the file to move to (must be from a tell call)
origin	can be any of the following: Note: not all are valid for all filetypes. SEEK_SET - Beginning of file SEEK_CUR - Current position of the file pointer SEEK_END - End of file

Returns

true on successful seek and false on a failed seek.

Definition at line 701 of file InputFile.h.

{
    if(file == NULL)
    {
        // Could not see since no file was specified.
        return(false);
    }
    return (file->ifseek(offset, origin));
}

References InputFile::ifseek().

iftell()

int64_t iftell ( IFILE file )

inline

Get current position in the file.

Can be fed back into ifseek.

Parameters

file	file to perform tell on - IFILE is a pointer to an InputFile object

Returns

current position in the file, -1 indicates an error.

Definition at line 682 of file InputFile.h.

{
    if(file == NULL)
    {
        return(-1);
    }
    return (file->iftell());
}

References InputFile::iftell().

Referenced by SamFile::GetCurrentPosition().

ifwrite()

unsigned int ifwrite ( IFILE file, const void * buffer, unsigned int size )

inline

Write the specified number of bytes from the specified buffer into the file.

Parameters

file	file to write to - IFILE is a pointer to an InputFile object
buffer	buffer containing size bytes to write to the file.
size	number of bytes to write

Returns

number of bytes written

Definition at line 669 of file InputFile.h.

{
    if(file == NULL)
    {
        // No file specified, so retun 0 bytes written.
        return(0);
    }
    return(file->ifwrite(buffer, size));
}

References InputFile::ifwrite().

Referenced by GlfHeader::write(), GlfRefSection::write(), and SamRecord::writeRecordBuffer().

operator<<() [1/6]

InputFile & operator<< ( InputFile & stream, char ch )

inline

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
ch	character that should be written to the file.

Definition at line 786 of file InputFile.h.

{
    unsigned int numWritten = 
        stream.ifwrite(&ch, 1);
    if(1 != numWritten)
    {
        std::cerr << "Failed to stream to IFILE, expected 1, but only wrote " 
                  << numWritten << std::endl;
    }
    return(stream);
}

References InputFile::ifwrite().

operator<<() [2/6]

InputFile & operator<< ( InputFile & stream, const char * str )

inline

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
str	string containing what should be written to the file.

Definition at line 753 of file InputFile.h.

{
    unsigned int numExpected = strlen(str);
    unsigned int numWritten = 
        stream.ifwrite(str, numExpected);
    if(numExpected != numWritten)
    {
        std::cerr << "Failed to stream to IFILE, expected " 
                  << numExpected << " but only wrote "
                  << numWritten << std::endl;
    }
    return(stream);
}

References InputFile::ifwrite().

operator<<() [3/6]

InputFile & operator<< ( InputFile & stream, const std::string & str )

inline

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
str	string containing what should be written to the file.

Definition at line 736 of file InputFile.h.

{
    unsigned int numExpected = str.length();
    unsigned int numWritten = 
        stream.ifwrite(str.c_str(), numExpected);
    if(numExpected != numWritten)
    {
        std::cerr << "Failed to stream to IFILE, expected " 
                  << numExpected << " but only wrote "
                  << numWritten << std::endl;
    }
    return(stream);
}

References InputFile::ifwrite().

operator<<() [4/6]

InputFile & operator<<	(	InputFile &	stream,
		double	num )

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
num	number that should be written to the file.

Definition at line 413 of file InputFile.cpp.

{
    String val;
    val = num;
    stream << val;
    return(stream);
}

operator<<() [5/6]

InputFile & operator<<	(	InputFile &	stream,
		int	num )

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
num	number that should be written to the file.

Definition at line 422 of file InputFile.cpp.

{
    String val;
    val = num;
    stream << val;
    return(stream);
}

operator<<() [6/6]

InputFile & operator<<	(	InputFile &	stream,
		unsigned int	num )

Write to a file using streaming.

Parameters

stream	file to write to - IFILE is a pointer to an InputFile object
num	number that should be written to the file.

Definition at line 431 of file InputFile.cpp.

{
    String val;
    val = num;
    stream << val;
    return(stream);
}

operator>>()

IFILE operator>> ( IFILE stream, std::string & str )

inline

Read a line from a file using streaming.

Will not fail when the file hits EOF, so do not do: while(iFile >> iStr) unless within your loop you check for ifeof and break. Instead, do something like: while(!iFile->ifeof() && iFile >> iStr)

Parameters

stream	file to read from - IFILE is a pointer to an InputFile object
str	output string containing the line read from the file.

Definition at line 724 of file InputFile.h.

{
    str.clear();
    int ch;
    // not safe... newline handling?
    while ((ch = stream->ifgetc())!=EOF && (ch != '\n')) str.push_back(ch);
    return stream;
}

References InputFile::ifgetc().