C++ Class: InputFile

InputFile / IFILE

This is our class for file operations. It hides the underlying file structure from the user. That way code can generically open and operate on a file using the exact same interface without having to know if the file is standard, gzip, or bgzf format (for reading from a file - for reading from stdin and writing, the user has to specify which type to open).

The IFILE class is made to mimic FILE. THe typical way to use IFILE is to call the set of global methods contained in InputFile.h that take IFILE as a parameter

To use IFILE, add the following include to your file.

#include "InputFile.h"

Global IFILE Methods

See: http://csg.sph.umich.edu//mktrost/doxygen/current/InputFile_8h.html for documentation on the global IFILE methods.

InputFile Class Documentation

See: http://csg.sph.umich.edu//mktrost/doxygen/current/classInputFile.html

BGZF Notes

Newer BGZF files have a empty BGZF block at the end to mark the EOF. By default when opening BGZF Files for reading, the software requires the empty block and the fail opens if it is not there. To support files without the empty block, the following call must first be made:

 BgzfFileType::setRequireEofBlock(false);

With that call, the empty block is not checked for when opening the file.

stdin/stdout

This class can be used to read/write to stdin/stdout.

To use stdin/stdout, specify the filename as "-" and use the ifileCompression parameter in ifopen to specify the compression type.

NOTE: even when reading from stdin, you MUST specify the file type. It does not read from stdin to determine the compression type like it does for other files.

When writing programs that will use stdout and pipes to send input from one program to the next, make sure that all error, debug, or info messages are written to stderr/cerr and not stdout/cout.

Example

 // specify to open stdin for read.
 // replace the - with a filename in order to read from a file.
 const char* filename = "-";
 IFILE myFilePtr = ifopen(filename, "rb", InputFile::BGZF);
 if (myFilePtr == NULL)
 {
     std::cerr << "Failed to open the file\n";
 }
 else
 {
    // File was successfully opened.
    // Read the magic string.
    char magic[4];
    if(ifread(myFilePtr, magic, 4) != 4)
    {
       std::cerr << "Could not read 4 bytes from the file\n";
    }
    ifclose(myFilePtr);
    myFilePtr = NULL;
 }