InputFile.h File Reference

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

---

Detailed Description

Definition in file InputFile.h.

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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 518 of file InputFile.h.

References InputFile::ifclose().

Referenced by 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 577 of file InputFile.h.

References InputFile::ifeof().

Referenced by GlfFile::isEOF(), SamFile::IsEOF(), GlfRefSection::read(), 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 553 of file InputFile.h.

References InputFile::ifgetc().

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

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 500 of file InputFile.h.

References InputFile::isOpen().

Referenced by GlfFile::openForRead(), SamFile::OpenForRead(), GlfFile::openForWrite(), SamFile::OpenForWrite(), and BamIndex::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 282 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 538 of file InputFile.h.

References InputFile::ifread().

Referenced by SamFile::OpenForRead(), GlfRefSection::read(), GlfRecord::read(), GlfHeader::read(), BamIndex::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 565 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 624 of file InputFile.h.

References InputFile::ifseek().

Referenced by SamFile::readIndexedRecord().

{
    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 605 of file InputFile.h.

References InputFile::iftell().

Referenced by SamFile::GetCurrentPosition(), and SamFile::readIndexedRecord().

{
    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 592 of file InputFile.h.

References InputFile::ifwrite().

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

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

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

Read a line from a file using streaming.

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 643 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;
}