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| | The '''FastQFile''' class allows a user to easily read/validate a fastq file. | | The '''FastQFile''' class allows a user to easily read/validate a fastq file. |
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| − | === Public Class Methods ===
| + | Documentation on this class is available at: http://www.sph.umich.edu/csg/mktrost/doxygen/current/classFastQFile.html |
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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;" '''SamFile Class Methods'''
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| − | ! Method Name !! Description
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| − | |-
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| − | | <code>FastQFile::FastQFile(int minReadLength = 10, int maxReportedErrors = 20)</code>
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| − | | Initializes the FastQFile class setting the minimum length that a base sequence must be for it to be valid to minReadLength and setting the maximum number of errors that should be reported in detail before suppressing the errors to maxReportedErrors.
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| − | |-
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| − | | <code> void FastQFile::disableMessages()</code>
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| − | | Disables cout messages. This does not include the Base Composition. Those are turned on/off based with a parameter to validateFastQFile.
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| − | |-
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| − | | <code>void FastQFile::enableMessages()</code>
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| − | |Enables cout messages. This does not include the Base Composition. Those are turned on/off based on a parameter to validateFastQFile.
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| − | |-
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| − | | <code>void FastQFile::setQuitAfterErrorNum(int quitAfterErrorNum)</code>
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| − | | Set the number of errors after which to quit reading/validating a file. (Defaults to -1)
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| − | -1 indicates to not quit until the entire file has been read/validated.
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| − | | |
| − | 0 indicates to quit without reading/validating anything.
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| − | |-
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| − | | <code>FastQStatus FastQFile::openFile(const char* fileName, BaseAsciiMap::SPACE_TYPE spaceType = BaseAsciiMap::UNKNOWN)</code>
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| − | | Open the specified fastq file with the specified base space type which defaults to UNKOWN (base the decision on the first character of the sequence).
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| − | | |
| − | Returns FastQStatus to indicate if the open was successful or not.
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| − | |-
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| − | | <code>FastQStatus FastQFile::closeFile()</code>
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| − | | Close the opened fastq file.
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| − | Returns FastQStatus to indicate if the close was successful or not.
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| − | |-
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| − | | <code>bool FastQFile::isOpen()</code>
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| − | | Returns true if a fastq file is open, false if one is not open.
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| − | |-
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| − | | <code>bool FastQFile::isEof()</code>
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| − | | Returns true if it is the end of the file, false if not.
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| − | |-
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| − | | <code>bool FastQFile::keepReadingFile()</code>
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| − | | Returns true if the file should continue to be read. Returns false on EOF or on a read error (corrupt gzip files never indicate EOF).
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| − | This method should be used for loops that continually read sequences instead of FastQFile::isEof()
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| − | |-
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| − | | <code>FastQStatus FastQFile::validateFastQFile(const String &filename, bool printBaseComp, BaseAsciiMap::SPACE_TYPE spaceType)</code>
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| − | | Validates the specified fastq file using the specified [[C++ Class: BaseAsciiMap#Public Class Enums|SpaceType]], printing the base composition if specified by printBaseComp.
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| − | Returns the fastq validation status - SUCCESS on a successfully validated fastq file.
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| − | | |
| − | Invalid error messages are printed to cout until maxReportedErrors is hit.
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| − | |-
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| − | | <code>FastQStatus FastQFile::readFastQSequence()</code>
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| − | | Read the next fastq sequence from the file
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| − | Returns FASTQ_SUCCESS if it was successfully read and was valid. Otherwise the failure status is returned.
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| − | | |
| − | Invalid error messages are printed to cout until maxReportedErrors is hit.
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| − | |-
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| − | | <code>BaseAsciiMap::SPACE_TYPE FastQFile::getSpaceType()</code>
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| − | | Return the [[C++ Class: BaseAsciiMap#Public Class Enums|SpaceType]] for the File
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| − | |-
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| − | |}
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| − | | |
| − | === Public Class Attributes ===
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| − | These attributes allow access to the contents of the last read fastq sequence. They are public <code>String</code> variables in order to avoid copying the strings.
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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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| − | ! Attribute !! Description
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| − | |-
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| − | | <code>myRawSequence</code>
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| − | | <code>String</code> containing the raw sequence for the last fastq sequence that was read.
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| − | |-
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| − | | <code>mySequenceIdLine</code>
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| − | | <code>String</code> containing the sequence identifier line for the last fastq sequence that was read.
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| − | |-
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| − | | <code>mySequenceIdentifier</code>
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| − | | <code>String</code> containing the sequence identifier for the last fastq sequence that was read.
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| − | |-
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| − | | <code>myPlusLine</code>
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| − | | <code>String</code> containing the plus line for the last fastq sequence that was read.
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| − | |-
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| − | | <code>myQualityString</code>
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| − | | <code>String</code> containing the quality string for the last fastq sequence that was read.
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| − | |}
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| − | | |
| − | === Public Class Enums ===
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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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| − | ! colspan="2"| enum FastQStatus
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| − | |-
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| − | ! Enum Value !! Description
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| − | |-
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| − | | FASTQ_SUCCESS
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| − | | method finished successfully.
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| − | |-
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| − | | FASTQ_FAILURE
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| − | | method failed to complete successfully.
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| − | |-
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| − | | FASTQ_INVALID
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| − | | sequence was invalid.
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| − | |}
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| | | | |
| | === Usage Example === | | === Usage Example === |
