Difference between revisions of "C++ Class: InputFile"

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= InputFile / IFILE =
 
= InputFile / IFILE =
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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.
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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).
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=== static Class Methods ===
 
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{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 
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|-style="background: #f2f2f2; text-align: center;"
 
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! Method Name !!  Description
 
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|-
 
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| void InputFile::setWriteFileType(FileTypeEnum fileType)
 
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|  Set the type of file to open when opening a file for write.
 
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Must be called prior to calling ifopen().
 
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Defaults to [[C++ Class: InputFile#ClassEnums|DEFAULT]] which determines the file type from the extension when opening a file for write.
 
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|}
 
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==== Using the static methods ====
 
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Here is an example of using setWriteFileType (writes a glf as a standard file rather than in bgzf which would be the default):
 
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<source lang="cpp">
 
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    InputFile::setWriteFileType(InputFile::STD);
 
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    std::string filename = "results/stdFile.glf";
 
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    filePtr = ifopen(filename.c_str(), "wt");
 
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    assert(filePtr != NULL);
 
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    assert(ifwrite(filePtr,
 
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                  IFILE_Test::TEST_FILE_CONTENTS.c_str(),
 
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                  IFILE_Test::TEST_FILE_CONTENTS.length())
 
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          == IFILE_Test::TEST_FILE_CONTENTS.length());
 
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    assert(ifclose(filePtr) == 0);
 
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</source>
 
  
  
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! Enum Value !!  Description
 
! Enum Value !!  Description
 
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! colspan="2"| enum FileTypeEnum
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! colspan="2"| enum ifileCompression
 
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| DEFAULT
 
| DEFAULT
 
| Use the default method for determining file type.
 
| Use the default method for determining file type.
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Opens as UNCOMPRESSED unless the filename ends in ".gz", then opened as GZIP
 
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| STD
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| UNCOMPRESSED
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| Standard File Type.
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| Standard Uncompressed File Type.
 
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| GZ
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| GZIP
 
| Gzip File Type.
 
| Gzip File Type.
 
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Revision as of 18:05, 23 June 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 (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.

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