FastQValidator - Revision history

Ppwhite: /* Return Value */

2017-02-02T15:00:06Z

Return Value

← Older revision		Revision as of 11:00, 2 February 2017
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	* 0 - the fastq file is valid.		* 0 - the fastq file is valid.
	* < 0 - invalid options specified.		* < 0 - invalid options specified.
	* > 0 - fastq file did not validate succesfully. One of the [http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classFastQStatus.html FastQStatus] failure values is returned		* > 0 - fastq file did not validate succesfully. One of the [http://csg.sph.umich.edu//mktrost/doxygen/current/classFastQStatus.html FastQStatus] failure values is returned

	== FastQ Validator Output ==		== FastQ Validator Output ==

Mktrost at 16:48, 13 November 2012

2012-11-13T16:48:00Z

← Older revision		Revision as of 12:48, 13 November 2012
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	[[Media:fastQValidatorLibStatGen.0.1.1.tgz\|fastQValidatorLibStatGen.0.1.1.tgz‎]] - Released 10/19/2012		[[Media:fastQValidatorLibStatGen.0.1.1a.tgz\|fastQValidatorLibStatGen.0.1.1a.tgz‎]] - Released 11/13/2012

	'''fastQValidatorLibStatGen.0.1.1 Release ~~Notes~~'''		'''fastQValidatorLibStatGen.0.1.1a Release Notes'''
	* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.3]]		* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.5]] (update for this version)
	* Contains: [[#Release of just fastQValidator (does not include libStatGen)\|fastQValidator version 0.1.1]]		* Contains: [[#Release of just fastQValidator (does not include libStatGen)\|fastQValidator version 0.1.1]] (same as full release 0.1.1)
	** Validates a fastq file with options to print additional information.
			'''Older Releases'''
			* [[Media:fastQValidatorLibStatGen.0.1.1.tgz\|fastQValidatorLibStatGen.0.1.1.tgz‎]] - Released 10/19/2012
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.3]]
			** Contains: [[#Release of just fastQValidator (does not include libStatGen)\|fastQValidator version 0.1.1]]
			*** Validates a fastq file with options to print additional information.

	=== Release of just fastQValidator (does not include libStatGen) ===		=== Release of just fastQValidator (does not include libStatGen) ===

Mktrost: /* Release of just fastQValidator (does not include libStatGen) */

2012-10-22T14:07:37Z

Release of just fastQValidator (does not include libStatGen)

← Older revision		Revision as of 10:07, 22 October 2012
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	'''fastQValidator.0.1.1 Release Notes'''		'''fastQValidator.0.1.1 Release Notes'''
	* Validates a fastq file with options to print additional information.		* Validates a fastq file with options to print additional information.
			* Adds option to output average qualities


			'''Older Releases'''
			*[[Media:fastQValidator.0.0.1.tgz\|fastQValidator.0.0.1.tgz]]
			** Validates a fastq file with options to print additional information.

	=== Using github ===		=== Using github ===

Mktrost: /* Where to find it */

2012-10-19T15:05:33Z

Where to find it

@@ Line 12: / Line 12: @@
 == Where to find it ==
 This command line tool can be obtained via:
-* Release Download '''coming soon'''
+* Release Download
 * github: https://github.com/statgen/fastQValidator
 ** Current development version
@@ Line 19: / Line 19: @@
 === Releases ===
-Release downloads are '''Coming Soon'''.
+If you prefer to run the last official release rather than the latest development version, you can download that here.

Dan Bolser: /* Building */

2012-09-18T19:27:43Z

Building

← Older revision		Revision as of 15:27, 18 September 2012
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	After obtaining the fastQValidator repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>fastQValidator</code>, in the <code>fastQValidator/bin/</code> directory, the debug executable in the <code>fastQValidator/bin/debug/</code> directory, and the profiling executable in the <code>fastQValidator/bin/profile/</code> directory.		After obtaining the fastQValidator repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>fastQValidator</code>, in the <code>fastQValidator/bin/</code> directory, the debug executable in the <code>fastQValidator/bin/debug/</code> directory, and the profiling executable in the <code>fastQValidator/bin/profile/</code> directory.

	'''NOTE:''' you should install the [[libStatGen]] package (or just check it out from Git) in order to compile this.		'''NOTE:''' you should install the [[C++ Library: libStatGen\|libStatGen]] package (or just check it out from Git) in order to compile this.

	== Valid FastQ File Requirements ==		== Valid FastQ File Requirements ==

Dan Bolser: /* Building */ This tripped me up for a while.

2012-09-18T19:26:03Z

Building: This tripped me up for a while.

← Older revision		Revision as of 15:26, 18 September 2012
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	After obtaining the fastQValidator repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>fastQValidator</code>, in the <code>fastQValidator/bin/</code> directory, the debug executable in the <code>fastQValidator/bin/debug/</code> directory, and the profiling executable in the <code>fastQValidator/bin/profile/</code> directory.		After obtaining the fastQValidator repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>fastQValidator</code>, in the <code>fastQValidator/bin/</code> directory, the debug executable in the <code>fastQValidator/bin/debug/</code> directory, and the profiling executable in the <code>fastQValidator/bin/profile/</code> directory.

			'''NOTE:''' you should install the [[libStatGen]] package (or just check it out from Git) in order to compile this.

	== Valid FastQ File Requirements ==		== Valid FastQ File Requirements ==

Mktrost at 22:13, 29 May 2012

2012-05-29T22:13:48Z

← Older revision		Revision as of 18:13, 29 May 2012
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	overwrites the printableErrors option.		overwrites the printableErrors option.
	--baseComposition : Print the Base Composition Statistics.		--baseComposition : Print the Base Composition Statistics.
	--disableSeqIDCheck : Disable the unique sequence identifier check.		--avgQual : Print the average phred quality per cycle & overall average quality.
			--disableSeqIDCheck : Disable the unique sequence identifier check.
	Use this option to save memory since the sequence id		Use this option to save memory since the sequence id
	check uses a lot of memory.		check uses a lot of memory.
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	1 5.00 95.00 0.00 0.00 0.00 20		1 5.00 95.00 0.00 0.00 0.00 20
	2 5.00 0.00 5.00 90.00 0.00 20		2 5.00 0.00 5.00 90.00 0.00 20

			Phred Quality by Index are printed if --avgQual is set to ON in a version after May 29, 2012. Only valid qualities are included in these averages. For Example:
			<pre>
			Average Phred Quality by Read Index (starts at 0):
			Read Index Average Quality
			0 44.10
			1 45.55
			2 51.11
			3 47.68
			4 47.37

			Overall Average Phred Quality = 50.40
			</pre>


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	*Prints a summary of the total number of errors.		*Prints a summary of the total number of errors.
	*Prints the total number of lines processed as well as the total number of sequences processed.		*Prints the total number of lines processed as well as the total number of sequences processed.
			* (May 29, 2012) Average Phred Quality can be reported by cycle & overall.

Mktrost: /* Additional Wishlist - Not Implemented */

2012-05-29T22:08:08Z

Additional Wishlist - Not Implemented

← Older revision		Revision as of 18:08, 29 May 2012
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	*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).		*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
	*Report average read quality score.
	*AutoDetect 64/33 illumina/standard quality scores.		*AutoDetect 64/33 illumina/standard quality scores.


	== Discussion ==		== Discussion ==

Mktrost at 18:45, 7 September 2011

2011-09-07T18:45:14Z

← Older revision		Revision as of 14:45, 7 September 2011
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	[[Category:C++]]		[[Category:C++]]
	[[Category:Software]]		[[Category:Software]]
	[[Category:LibStatGen ~~FastQ~~]]		[[Category:LibStatGen FASTQ]]
	= fastQValidator Overview =		= fastQValidator Overview =

Mktrost at 18:44, 7 September 2011

2011-09-07T18:44:54Z

← Older revision		Revision as of 14:44, 7 September 2011
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	[[Category:C++]]		[[Category:C++]]
	[[Category:Software]]		[[Category:Software]]
	[[Category:~~FastQValidator~~]]		[[Category:LibStatGen FastQ]]
	= fastQValidator Overview =		= fastQValidator Overview =