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

Include dependency graph for InputFile.h:

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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.

Detailed Description

Definition in file InputFile.h.

Function Documentation

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.

References InputFile::ifclose().

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

{
    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);
}

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.

References InputFile::ifeof().

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

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

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.

References InputFile::ifgetc().

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

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.

References InputFile::ifgetline().

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

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.

References InputFile::isOpen().

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

{
    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;
}

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.

References ifwrite().

{
    String buffer;

    va_list  ap;
    va_start(ap, format);

    buffer.vprintf(format, ap);

    va_end(ap);

    return ::ifwrite(output, (const char *) buffer, buffer.Length());
}

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.

References InputFile::ifread().

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

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

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.

References InputFile::ifrewind().

Referenced by SamFile::OpenForRead().

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

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.

References InputFile::ifseek().

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

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.

References InputFile::iftell().

Referenced by SamFile::GetCurrentPosition().

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

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.

References InputFile::ifwrite().

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

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

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.

References InputFile::ifwrite().

{
    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);
}

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.

References InputFile::ifwrite().

{
    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);
}

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);
}

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);
}

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);
}

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.

References InputFile::ifwrite().

{
    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);
}

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.

References InputFile::ifgetc().

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

Classes

Typedefs

Functions

Detailed Description

Function Documentation