C++ Class: FastQFile - Revision history

Ppwhite: /* Reading/Validating FastQ Files In Your Program */

2017-02-02T14:58:18Z

Reading/Validating FastQ Files In Your Program

← Older revision		Revision as of 10:58, 2 February 2017
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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.

	Documentation on this class is available at: http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classFastQFile.html		Documentation on this class is available at: http://csg.sph.umich.edu//mktrost/doxygen/current/classFastQFile.html

	=== Usage Example ===		=== Usage Example ===

Mktrost: /* Additional Features */ update fastqvalidator link

2011-09-07T18:02:16Z

Additional Features: update fastqvalidator link

← Older revision		Revision as of 14:02, 7 September 2011
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	*Consumes gzipped and uncompressed text files transparently.		*Consumes gzipped and uncompressed text files transparently.
	*Prints error messages for errors up to the configurable maximum number of reportable errors.		*Prints error messages for errors up to the configurable maximum number of reportable errors.
	*[[~~FastQ Validator~~\|Standalone Program for Validating a FastQ File]]		*[[FastQValidator\|Standalone Program for Validating a FastQ File]]


	== Additional Wishlist - Not Implemented ==		== Additional Wishlist - Not Implemented ==
	*Add an option that would reject raw sequence and quality strings that wrap over multiple lines. It would only allow 1 line per raw sequence/quality string.		*Add an option that would reject raw sequence and quality strings that wrap over multiple lines. It would only allow 1 line per raw sequence/quality string.
	*Maybe report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).		*Maybe report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).

Mktrost: Update for doxygen

2011-09-07T18:00:49Z

Update for doxygen

@@ Line 6: / Line 6: @@
 The '''FastQFile''' class allows a user to easily read/validate a fastq file.
-=== Public Class Methods ===
+Documentation on this class is available at: http://www.sph.umich.edu/csg/mktrost/doxygen/current/classFastQFile.html
 === Usage Example ===

Mktrost at 20:20, 17 November 2010

2010-11-17T20:20:28Z

← Older revision		Revision as of 16:20, 17 November 2010
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	~~[[Category:Software]]~~
	[[Category:C++]]		[[Category:C++]]
	[[Category:libStatGen]]		[[Category:libStatGen]]

Mktrost at 05:43, 2 November 2010

2010-11-02T05:43:52Z

← Older revision		Revision as of 01:43, 2 November 2010
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			[[Category:Software]]
			[[Category:C++]]
			[[Category:libStatGen]]
			[[Category:libStatGen FASTQ]]

	== Reading/Validating FastQ Files In Your Program ==		== Reading/Validating FastQ Files In Your Program ==
	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.

Mktrost at 17:34, 6 May 2010

2010-05-06T17:34:02Z

← Older revision		Revision as of 13:34, 6 May 2010
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	\| <code>bool FastQFile::isEof()</code>		\| <code>bool FastQFile::isEof()</code>
	\| Returns true if it is the end of the file, false if not.		\| Returns true if it is the end of the file, false if not.
			\|-
			\| <code>bool FastQFile::keepReadingFile()</code>
			\| 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).
			This method should be used for loops that continually read sequences instead of FastQFile::isEof()
	\|-		\|-
	\| <code>FastQStatus FastQFile::validateFastQFile(const String &filename, bool printBaseComp, BaseAsciiMap::SPACE_TYPE spaceType)</code>		\| <code>FastQStatus FastQFile::validateFastQFile(const String &filename, bool printBaseComp, BaseAsciiMap::SPACE_TYPE spaceType)</code>
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	}		}
	// Keep reading the file until there are no more fastq sequences to process.		// Keep reading the file until there are no more fastq sequences to process.
	while (!fastQFile.~~isEof~~())		while (fastQFile.keepReadingFile())
	{		{
	// Read one sequence. This call will read all the lines for		// Read one sequence. This call will read all the lines for

Mktrost at 14:26, 15 April 2010

2010-04-15T14:26:59Z

@@ Line 142: / Line 142: @@
 == Validation Criteria Used For Reading a Sequence ==
-{| class="wikitable" style="width:100%"
+[[FastQ Validation Criteria]]
 == Reading Sequence Assumptions ==

Mktrost at 22:31, 6 April 2010

2010-04-06T22:31:41Z

← Older revision		Revision as of 18:31, 6 April 2010
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	\|-		\|-
	\| <code>FastQStatus FastQFile::validateFastQFile(const String &filename, bool printBaseComp, BaseAsciiMap::SPACE_TYPE spaceType)</code>		\| <code>FastQStatus FastQFile::validateFastQFile(const String &filename, bool printBaseComp, BaseAsciiMap::SPACE_TYPE spaceType)</code>
	\| Validates the specified fastq file using the specified SpaceType, printing the base composition if specified by printBaseComp.		\| Validates the specified fastq file using the specified [[C++ Class: BaseAsciiMap#Public Class Enums\|SpaceType]], printing the base composition if specified by printBaseComp.
	Returns the fastq validation status - SUCCESS on a successfully validated fastq file.		Returns the fastq validation status - SUCCESS on a successfully validated fastq file.

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	\|-		\|-
	\| <code>BaseAsciiMap::SPACE_TYPE FastQFile::getSpaceType()</code>		\| <code>BaseAsciiMap::SPACE_TYPE FastQFile::getSpaceType()</code>
	\| Return the [[C++ Class: BaseAsciiMap\|~~BaseAsciiMap::~~SpaceType]] for the File		\| Return the [[C++ Class: BaseAsciiMap#Public Class Enums\|SpaceType]] for the File
	\|-		\|-
	\|}		\|}

Mktrost at 22:11, 6 April 2010

2010-04-06T22:11:49Z

Show changes

Mktrost: Created page with '== Reading/Validating FastQ Files In Your Program == The '''FastQFile''' class allows a user to easily read/validate a fastq file. === Class Methods === {| style="margin: 1em 1…'

2010-04-06T21:40:22Z

Created page with '== Reading/Validating FastQ Files In Your Program == The '''FastQFile''' class allows a user to easily read/validate a fastq file. === Class Methods === {| style="margin: 1em 1…'

New page

== Reading/Validating FastQ Files In Your Program ==
The '''FastQFile''' class allows a user to easily read/validate a fastq file.

=== 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;" '''SamFile Class Methods'''
! Method Name !! Description
|-
| <code>FastQFile::FastQFile(int minReadLength, int maxReportedErrors)</code>
|
|-
|}

=== 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;"
! colspan="2"| enum FastQStatus
|-
! Enum Value !! Description
|-
| FASTQ_SUCCESS
| method finished successfully.
|-
| FASTQ_FAILURE
| method failed to complete successfully.
|-
| FASTQ_INVALID
| sequence was invalid.
|}

=== Usage Example ===

<source lang="cpp">

</source>