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, 17:18, 12 March 2010
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| ERROR on Line 33: No Sequence Identifier specified before the comment. | | ERROR on Line 33: No Sequence Identifier specified before the comment. |
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| + | |
| + | == Use of the FastQFile class === |
| + | Generally this class is used to read a fastq file and perform operations on the sequences. |
| + | Here is an example of how this would be done. |
| + | |
| + | bool <yourMethod>() |
| + | { |
| + | String filename = <your filename>; |
| + | BaseAsciiMap::SPACE_TYPE spaceType = <BASE_SPACE/COLOR_SPACE>; |
| + | // Open the fastqfile. |
| + | if(openFile(filename, spaceType) != FASTQ_SUCCESS) |
| + | { |
| + | // Failed to open the specified file. |
| + | // Report the error and exit (handled by error). |
| + | error("Failed to open file: %s", filename.c_str()); |
| + | return (false); |
| + | } |
| + | // Keep reading the file until there are no more fastq sequences to process. |
| + | while (!ifeof(myFile)) |
| + | { |
| + | // Read one sequence. This call will read all the lines for |
| + | // one sequence. |
| + | FastQFile::FastQStatus = readFastQSequence; |
| + | ///////////////////////////////////////////////////////////////// |
| + | // NOTE: It is up to you if you want to process only for success: |
| + | // if(readFastQSequence() == FASTQ_SUCCESS) |
| + | // or for FASTQ_SUCCESS and FASTQ_INVALID: |
| + | // if(readFastQSequence() != FASTQ_FAILURE) |
| + | // Do NOT try to process on a FASTQ_FAILURE |
| + | ///////////////////////////////////////////////////////////////// |
| + | if(readFastQSequence() == FASTQ_SUCCESS) |
| + | { |
| + | // The sequence is valid. |
| + | <Your Processing Here> |
| + | } |
| + | } |
| + | // Finished processing all of the sequences in the file. |
| + | // Close the input file. |
| + | closeFile(); |
| + | return(true/false); // It is up to you to determine what is considered success/failure. |
| + | } |
| | | |
| == Validation Criteria Used For Reading a Sequence == | | == Validation Criteria Used For Reading a Sequence == |