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. | ||
| + | |||
| + | |||
| + | === static Class Methods === | ||
| + | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | ||
| + | |-style="background: #f2f2f2; text-align: center;" | ||
| + | ! Method Name !! Description | ||
| + | |- | ||
| + | | void InputFile::setWriteFileType(FileTypeEnum fileType) | ||
| + | | Set the type of file to open when opening a file for write. | ||
| + | Must be called prior to calling ifopen(). | ||
| + | |||
| + | Defaults to [[C++ Class: InputFile#ClassEnums|DEFAULT]] which determines the file type from the extension when opening a file for write. | ||
| + | |} | ||
| Line 10: | Line 23: | ||
| ***NEEDS TO BE FILLED IN*** | | ***NEEDS TO BE FILLED IN*** | ||
| ***NEEDS TO BE FILLED IN*** | | ***NEEDS TO BE FILLED IN*** | ||
| + | |} | ||
| + | |||
| + | === Class Enums === | ||
| + | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | ||
| + | |-style="background: #f2f2f2; text-align: center;" | ||
| + | |||
| + | ! Enum Value !! Description | ||
| + | |- | ||
| + | ! colspan="2"| enum FileTypeEnum | ||
| + | |- | ||
| + | | DEFAULT | ||
| + | | Use the default method for determining file type. | ||
| + | |- | ||
| + | | STD | ||
| + | | Standard File Type. | ||
| + | |- | ||
| + | | GZ | ||
| + | | Gzip File Type. | ||
| + | |- | ||
| + | | BGZF | ||
| + | | bgzf File Type. | ||
|} | |} | ||
Revision as of 11:49, 20 May 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.
static Class Methods
| Method Name | Description |
|---|---|
| void InputFile::setWriteFileType(FileTypeEnum fileType) | Set the type of file to open when opening a file for write.
Must be called prior to calling ifopen(). Defaults to DEFAULT which determines the file type from the extension when opening a file for write. |
Public Class Methods
| Method Name | Description |
|---|---|
| ***NEEDS TO BE FILLED IN*** | ***NEEDS TO BE FILLED IN*** |
Class Enums
| Enum Value | Description |
|---|---|
| enum FileTypeEnum | |
| DEFAULT | Use the default method for determining file type. |
| STD | Standard File Type. |
| GZ | 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.
