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 (at least for reading - for writing the user has to specify which type to open).

Public Class Methods

Method Name	Description
***NEEDS TO BE FILLED IN***	***NEEDS TO BE FILLED IN***

Class Enums

Enum Value	Description
enum ifileCompression
DEFAULT	Use the default method for determining file type. Opens as UNCOMPRESSED unless the filename ends in ".gz", then opened as GZIP
UNCOMPRESSED	Standard Uncompressed File Type.
GZIP	Gzip File Type.
BGZF	bgzf File Type.

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.