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| | + | [[Category:C++]] |
| | + | [[Category:libStatGen]] |
| | + | [[Category:libStatGen general]] |
| | + | |
| | = 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 (for reading from a file - for reading from stdin and writing, the user has to specify which type to open). | | 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). |
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| | | | |
| | === Global IFILE Methods === | | === Global IFILE 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
| |
| − | |-
| |
| − | | <code>IFILE ifopen(const char * filename, const char * mode, InputFile::ifileCompression compressionMode = InputFile::DEFAULT)</code>
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| − | | Open the file with the specified name with the specified mode.
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| − | A filename = "-" indicates stdin/stdout.
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| − |
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| − | When reading a file (not from stdin), the file compression type is determined by reading the file.
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| − |
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| − | When reading from stdin and writing anywhere the file compression type is determined by the passed in parameter.
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| − | |-
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| − | | <code>int ifclose(IFILE file)</code>
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| − | | Close the file.
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| − | |-
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| − | | <code>unsigned int ifread(IFILE file, void * buffer, unsigned int size)</code>
| |
| − | | Reads up to size bytes from the file into the buffer. Returns the number of bytes read.
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| − | |-
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| − | | <code>int ifgetc(IFILE file)</code>
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| − | | Reads and returns 1 character from the file. Returns EOF on error/end of file.
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| − | |-
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| − | | <code>void ifrewind(IFILE file)</code>
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| − | | Go to the beginning of the file (cannot be done for stdin/stdout).
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| − | |-
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| − | | <code> int ifeof(IFILE file)</code>
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| − | | Return 0 if it is not the end of the file, otherwise returns non-zero.
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| − | |-
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| − | | <code>unsigned int ifwrite(IFILE file, const void * buffer, unsigned int size)</code>
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| − | | Write the size bytes from buffer into the file.
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| − | |-
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| − | | <code>long int iftell(IFILE file)</code>
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| − | | Tell the current position in the file. Can be fed back into ifseek.
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| − | |-
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| − | | <code>bool ifseek(IFILE file, long int offset, int origin)</code>
| |
| − | | Go to the specified position (result from an iftell) in the file (cannot be done for stdin/stdout).
| |
| − | |}
| |
| | | | |
| − | === Class Enums ===
| + | See: http://csg.sph.umich.edu//mktrost/doxygen/current/InputFile_8h.html for documentation on the global IFILE methods. |
| − | {| 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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| | | | |
| − | ! Enum Value !! Description
| + | === InputFile Class Documentation === |
| − | |-
| |
| − | ! colspan="2"| enum ifileCompression
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| − | |-
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| − | | DEFAULT
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| − | | 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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| − | |-
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| − | | UNCOMPRESSED
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| − | | Standard, Uncompressed File Type.
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| − | |-
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| − | | GZIP
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| − | | Gzip File Type.
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| − | |-
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| − | | BGZF
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| − | | bgzf File Type.
| |
| − | |}
| |
| | | | |
| | + | See: http://csg.sph.umich.edu//mktrost/doxygen/current/classInputFile.html |
| | | | |
| | === BGZF Notes === | | === BGZF Notes === |
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| | const char* filename = "-"; | | const char* filename = "-"; |
| | IFILE myFilePtr = ifopen(filename, "rb", InputFile::BGZF); | | IFILE myFilePtr = ifopen(filename, "rb", InputFile::BGZF); |
| − | if (myFilePtr != NULL) | + | if (myFilePtr == NULL) |
| | { | | { |
| | std::cerr << "Failed to open the file\n"; | | std::cerr << "Failed to open the file\n"; |
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| | } | | } |
| | </source> | | </source> |
| − |
| |
| − | [[Category:C++]]
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| − | [[Category:libcsg]]
| |
