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.
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 581 of file InputFile.h.

References InputFile::ifclose().

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

00582 {
00583     if(file == NULL)
00584     {
00585         // NULL Pointer passed in, so return 0, since no file is open, so
00586         // does not need to be closed.
00587         return(0);
00588     }
00589     int result = file->ifclose();
00590     delete file;
00591     file = NULL;
00592     return(result);
00593 }

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 655 of file InputFile.h.

References InputFile::ifeof().

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

00656 {
00657     if(file == NULL)
00658     {
00659         // No file, so that is considered to be EOF, so return 1.
00660         return(1);
00661     }
00662     return(file->ifeof());
00663 }

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 616 of file InputFile.h.

References InputFile::ifgetc().

00617 {
00618     if(file == NULL)
00619     {
00620         // return eof since there is no file.
00621         return(EOF);
00622     }
00623     return(file->ifgetc());
00624 }

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 631 of file InputFile.h.

References InputFile::ifgetline().

00632 {
00633     if(file == NULL)
00634     {
00635         // return eof since there is no file.
00636         return(EOF);
00637     }
00638     return(file->ifgetline(buffer, max));
00639 }

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 563 of file InputFile.h.

References InputFile::isOpen().

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

00565 {
00566     IFILE file = new InputFile(filename, mode, compressionMode);
00567     if (!file->isOpen())
00568     {
00569 
00570         // Not open, so delete the file, and return null.
00571         delete file;
00572         file = NULL;
00573     }
00574     return file;
00575 }

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 399 of file InputFile.cpp.

References ifwrite().

00400 {
00401     String buffer;
00402 
00403     va_list  ap;
00404     va_start(ap, format);
00405 
00406     buffer.vprintf(format, ap);
00407 
00408     va_end(ap);
00409 
00410     return ::ifwrite(output, (const char *) buffer, buffer.Length());
00411 }

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 601 of file InputFile.h.

References InputFile::ifread().

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

00602 {
00603     if(file == NULL)
00604     {
00605         // No file was passed in, so 0 bytes were read.
00606         return(0);
00607     }
00608     return(file->ifread(buffer, size));
00609 }

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 643 of file InputFile.h.

References InputFile::ifrewind().

Referenced by SamFile::OpenForRead().

00644 {
00645     if(file == NULL)
00646     {
00647         return;
00648     }
00649     file->ifrewind();
00650 }

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 702 of file InputFile.h.

References InputFile::ifseek().

00703 {
00704     if(file == NULL)
00705     {
00706         // Could not see since no file was specified.
00707         return(false);
00708     }
00709     return (file->ifseek(offset, origin));
00710 }

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 683 of file InputFile.h.

References InputFile::iftell().

Referenced by SamFile::GetCurrentPosition().

00684 {
00685     if(file == NULL)
00686     {
00687         return(-1);
00688     }
00689     return (file->iftell());
00690 }

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 670 of file InputFile.h.

References InputFile::ifwrite().

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

00671 {
00672     if(file == NULL)
00673     {
00674         // No file specified, so retun 0 bytes written.
00675         return(0);
00676     }
00677     return(file->ifwrite(buffer, size));
00678 }

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 783 of file InputFile.h.

References InputFile::ifwrite().

00784 {
00785     unsigned int numWritten = 
00786         stream.ifwrite(&ch, 1);
00787     if(1 != numWritten)
00788     {
00789         std::cerr << "Failed to stream to IFILE, expected 1, but only wrote " 
00790                   << numWritten << std::endl;
00791     }
00792     return(stream);
00793 }

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 432 of file InputFile.cpp.

00433 {
00434     String val;
00435     val = num;
00436     stream << val;
00437     return(stream);
00438 }

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 423 of file InputFile.cpp.

00424 {
00425     String val;
00426     val = num;
00427     stream << val;
00428     return(stream);
00429 }

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 414 of file InputFile.cpp.

00415 {
00416     String val;
00417     val = num;
00418     stream << val;
00419     return(stream);
00420 }

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 750 of file InputFile.h.

References InputFile::ifwrite().

00751 {
00752     unsigned int numExpected = strlen(str);
00753     unsigned int numWritten = 
00754         stream.ifwrite(str, numExpected);
00755     if(numExpected != numWritten)
00756     {
00757         std::cerr << "Failed to stream to IFILE, expected " 
00758                   << numExpected << " but only wrote "
00759                   << numWritten << std::endl;
00760     }
00761     return(stream);
00762 }

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 733 of file InputFile.h.

References InputFile::ifwrite().

00734 {
00735     unsigned int numExpected = str.length();
00736     unsigned int numWritten = 
00737         stream.ifwrite(str.c_str(), numExpected);
00738     if(numExpected != numWritten)
00739     {
00740         std::cerr << "Failed to stream to IFILE, expected " 
00741                   << numExpected << " but only wrote "
00742                   << numWritten << std::endl;
00743     }
00744     return(stream);
00745 }

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 721 of file InputFile.h.

References InputFile::ifgetc().

00722 {
00723     str.clear();
00724     int ch;
00725     // not safe... newline handling?
00726     while ((ch = stream->ifgetc())!=EOF && (ch != '\n')) str.push_back(ch);
00727     return stream;
00728 }

InputFile.h File Reference

Classes

Typedefs

Functions

Detailed Description

Function Documentation