LibStatGen: FASTQ - Revision history

Ppwhite: /* Classes in the FASTQ Portion of Library */

2017-02-02T14:49:43Z

Classes in the FASTQ Portion of Library

← Older revision		Revision as of 10:49, 2 February 2017
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	\| Class used for reading/validating a fastq file.		\| Class used for reading/validating a fastq file.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classBaseCount.html BaseCount]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classBaseCount.html BaseCount]</code>
	\| Wrapper around an array that has one index per base and an extra index for a total count of all bases. This class is used to keep a count of the number of times each index has occurred. It can print a percentage of the occurrence of each base against the total number of bases.		\| Wrapper around an array that has one index per base and an extra index for a total count of all bases. This class is used to keep a count of the number of times each index has occurred. It can print a percentage of the occurrence of each base against the total number of bases.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>
	\| Class that tracks the composition of base by read location.		\| Class that tracks the composition of base by read location.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classFastQStatus.html FastQStatus]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classFastQStatus.html FastQStatus]</code>
	\| Status for FastQ operations.		\| Status for FastQ operations.
	\|}		\|}


	== FASTQ Output ==		== FASTQ Output ==

Mktrost: Add FastQStatus

2011-09-07T17:42:53Z

Add FastQStatus

← Older revision		Revision as of 13:42, 7 September 2011
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	\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>
	\| Class that tracks the composition of base by read location.		\| Class that tracks the composition of base by read location.
			\|-
			\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classFastQStatus.html FastQStatus]</code>
			\| Status for FastQ operations.
	\|}		\|}

Mktrost: Update links

2011-09-07T17:41:53Z

Update links

← Older revision		Revision as of 13:41, 7 September 2011
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	== Where to find the fastqFile Library and the FastQValidator ==		== Where to find the fastqFile Library and the FastQValidator ==
	~~They are~~ now ~~released as~~ part of ~~the statgen software~~. ~~Which can be downloaded~~ at~~: http://genome.sph.umich~~.~~edu/wiki/Software#Download~~
			The fastQ Library is now a part of [[C++ Library: libStatGen]].

			The FastQValidator is documented at [[FastQValidator]].

	== FASTQ Library Component for Reading and Validating FastQFiles ==		== FASTQ Library Component for Reading and Validating FastQFiles ==
	The software reads and validates fastq files in both compressed and uncompressed formats.		The software reads and validates fastq files in both compressed and uncompressed formats.

	The FASTQ component of the library is found in statgen/~~lib~~/fastq.		The FASTQ component of the library is found in libStatGen/fastq/.

			See https://github.com/statgen/libStatGen/commits/master/fastq for a list of the most recent updates to the development version of the FASTQ portion of the library.

	~~See~~ [[C++ Library: FASTQ Change Log]] ~~for a list of the most recent updates to the development version of the FASTQ portion of the library.~~		For the old change log, see: [[C++ Library: FASTQ Change Log]]

	=== Classes in the FASTQ Portion of Library ===		=== Classes in the FASTQ Portion of Library ===
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	\| Class used for reading/validating a fastq file.		\| Class used for reading/validating a fastq file.
	\|-		\|-
	\| <code>BaseCount</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseCount.html BaseCount]</code>
	\| Wrapper around an array that has one index per base and an extra index for a total count of all bases. This class is used to keep a count of the number of times each index has occurred. It can print a percentage of the occurrence of each base against the total number of bases.		\| Wrapper around an array that has one index per base and an extra index for a total count of all bases. This class is used to keep a count of the number of times each index has occurred. It can print a percentage of the occurrence of each base against the total number of bases.
	\|-		\|-
	\| <code>BaseComposition</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>
	\| Class that tracks the composition of base by read location.		\| Class that tracks the composition of base by read location.
	\|}		\|}
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	== FASTQ Output ==		== FASTQ Output ==
	When a sequence is read, error messages for the first maxReportedErrors are output for failed [[#Validation Criteria Used For Reading a Sequence\|Validation Criteria]].		When a sequence is read, error messages for the first maxReportedErrors are output for failed [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence\|Validation Criteria]].
	For Example:		For Example:
	ERROR on Line 25: The sequence identifier line was too short.		ERROR on Line 25: The sequence identifier line was too short.

Mktrost: moved StatGenLibrary: FASTQ to LibStatGen: FASTQ

2011-08-24T14:00:32Z

moved StatGenLibrary: FASTQ to LibStatGen: FASTQ

← Older revision	Revision as of 10:00, 24 August 2011
(No difference)

Mktrost at 20:20, 17 November 2010

2010-11-17T20:20:57Z

← 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 05:42, 2 November 2010

2010-11-02T05:42:14Z

← Older revision		Revision as of 01:42, 2 November 2010
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			[[Category:Software]]
			[[Category:C++]]
			[[Category:libStatGen]]
			[[Category:libStatGen FASTQ]]

	== Where to find the fastqFile Library and the FastQValidator ==		== Where to find the fastqFile Library and the FastQValidator ==
	They are now released as part of the statgen software. Which can be downloaded at: http://genome.sph.umich.edu/wiki/Software#Download		They are now released as part of the statgen software. Which can be downloaded at: http://genome.sph.umich.edu/wiki/Software#Download

Mktrost: /* Library Output */

2010-11-02T05:31:37Z

Library Output

← Older revision		Revision as of 01:31, 2 November 2010
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	== ~~Library~~ Output ==		== FASTQ Output ==
	When a sequence is read, error messages for the first maxReportedErrors are output for failed [[#Validation Criteria Used For Reading a Sequence\|Validation Criteria]].		When a sequence is read, error messages for the first maxReportedErrors are output for failed [[#Validation Criteria Used For Reading a Sequence\|Validation Criteria]].
	For Example:		For Example:
Line 31:		Line 31:
	ERROR on Line 29: First line of a sequence does not begin wtih @		ERROR on Line 29: First line of a sequence does not begin wtih @
	ERROR on Line 33: No Sequence Identifier specified before the comment.		ERROR on Line 33: No Sequence Identifier specified before the comment.


	== FastQValidator ==		== FastQValidator ==
	The [[FastQValidator]] was built using the FastQFile class. More details on that program are at the supplied link.		The [[FastQValidator]] was built using the FastQFile class. More details on that program are at the supplied link.

Mktrost at 05:31, 2 November 2010

2010-11-02T05:31:18Z

← Older revision		Revision as of 01:31, 2 November 2010
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	See [[C++ Library: FASTQ Change Log]] for a list of the most recent updates to the development version of the FASTQ portion of the library.		See [[C++ Library: FASTQ Change Log]] for a list of the most recent updates to the development version of the FASTQ portion of the library.

	=== Classes in the FASTQ Library ===		=== Classes in the FASTQ Portion of Library ===
	{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
	\|-style="background: #f2f2f2; text-align: center;"		\|-style="background: #f2f2f2; text-align: center;"

Mktrost at 05:18, 2 November 2010

2010-11-02T05:18:14Z

← Older revision		Revision as of 01:18, 2 November 2010
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	The FASTQ component of the library is found in statgen/lib/fastq.		The FASTQ component of the library is found in statgen/lib/fastq.

	See [[C++ Library: ~~libfqf~~ Change Log]] for a list of the most recent updates to the development version of the library.		See [[C++ Library: FASTQ Change Log]] for a list of the most recent updates to the development version of the FASTQ portion of the library.

	=== Classes in the FASTQ Library ===		=== Classes in the FASTQ Library ===

Mktrost: /* FastQValidator */

2010-11-02T05:14:18Z

FastQValidator

← Older revision		Revision as of 01:14, 2 November 2010
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	== FastQValidator ==		== FastQValidator ==
	The [[~~FastQ_Validator~~]] was built using the FastQFile class. More details on that program are at the supplied link.		The [[FastQValidator]] was built using the FastQFile class. More details on that program are at the supplied link.