Difference between revisions of "C++ Class: InputFile"
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= InputFile / IFILE = | = 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 ( | + | 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). |
Revision as of 16:12, 29 September 2010
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).
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.