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== Status ==
[[Category:C++]]
[[Category:Software]]
[[Category:LibStatGen FASTQ]]
= fastQValidator Overview =
The initial version of a [http://en.wikipedia.org/wiki/FASTQ_format FastQ] Validator is complete. It was built using the [[FastQFile]] class.
The fastQValidator validates the format of fastq files.
The initial version of a FASTQ Validator is complete. It was built using [[LibStatGen: FASTQ]] which is part of the [[C++ Library: libStatGen|libStatGen]] library.
Note: Since the FastQValidator checks for unique sequence names, it may use a large amount of memory - this can be disabled by specifying the --disableSeqIDCheck option
== Where to find it ==
This command line tool can be obtained via:
* Release Download
* github: https://github.com/statgen/fastQValidator
** Current development version
** Available for download or using git.
** Requires [[C++ Library: libStatGen]], available at: https://github.com/statgen/libStatGen
=== Releases ===
If you prefer to run the last official release rather than the latest development version, you can download that here.
There are two versions of the release, one that include libStatGen and one that does not. If you already have libStatGen installed and want to use your own copy, use the version that does not include libStatGen.
=== Full Release (includes libStatGen) ===
To install an official release, unpack the downloaded file (tar xvf), cd into the fastQValidator_x.x.x directory and type make all.
[[Media:fastQValidatorLibStatGen.0.1.1a.tgz|fastQValidatorLibStatGen.0.1.1a.tgz]] - Released 11/13/2012
'''fastQValidatorLibStatGen.0.1.1a Release Notes'''
* 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]] (same as full release 0.1.1)
'''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) ===
To install an official release, unpack the downloaded file (tar xvf), cd into the fastQValidator_x.x.x directory and type make all.
[[Media:fastQValidator.0.1.1.tgz|fastQValidator.0.1.1.tgz]] - Released 10/19/2012
'''fastQValidator.0.1.1 Release Notes'''
* 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 Git To Track the Current Development Version ====
===== Clone (get your own copy) =====
You can create your own git clone (copy) using:
git clone https://github.com/statgen/fastQValidator.git
or
git clone git://github.com/statgen/fastQValidator.git
Either of these commands create a directory called <code>fastQValidator</code> in the current directory.
Then just <code>cd fastQValidator</code> and [[fastQValidator#Building|compile]].
===== Get the latest Updates (update your copy) =====
To update your copy to the latest version (a major advantage of using git):
# <code>cd pathToYourCopy/fastQValidator</code>
# <code>make clean</code>
# <code>git pull</code>
# <code>make all</code>
=== Git Refresher ===
If you decide to use git, but need a refresher, see [[How To Use Git]] or [https://statgen.sph.umich.edu/wiki/How_To_Use_Git Notes on how to use git] (if you have access)
==== Downloading From GitHub Without Git ====
Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/fastQValidator/archives/master.
The downloaded tar file is named "statgen-fastQValidator-someHexNumber.tar.gz". The directory created when it is untared shares the same base name. I recommend that you do not change the name of the directory. If you want one called fastQValidator, create a link to this directory. The hex number in the directory name identifies the version of the repository that you downloaded and is necessary to easily troubleshoot any issues you encounter. If you must rename the directory, be sure to record the hex number that was on the download for future reference.
== Building ==
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 [[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 ==
A valid fastQ file meets the validation criteria specified in [[FastQFile#Validation Criteria Used For Reading a Sequence|FastQ File Validation]].
A valid fastQ file meets the validation criteria specified in [[FastQ Validation Criteria]].
== How to Use the fastQValidator Executable ==
== How to Use the fastQValidator Executable ==
=== Required Parameters ===
--file : FastQ filename with path to be prorcessed.
--file : FastQ filename with path to be processed.
=== Optional Parameters ===
--minReadLen : Minimum allowed read length (Defaults to 10).
--minReadLen : Minimum allowed read length (Defaults to 10).
--maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20).
--maxErrors : Number of errors to allow before quitting
--ignoreAllErrors : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option.
reading/validating the file.
-1 (default) indicates to not quit until
the entire file is read.
0 indicates not to read/validate anything
--printableErrors : Maximum number of errors to print before
suppressing them (Defaults to 20).
Different than maxErrors since
printableErrors will continue reading and
validating the file until the end, but
just doesn't print the errors.
--ignoreErrors : Ignore all errors (same as printableErrors = 0)
overwrites the printableErrors option.
--baseComposition : Print the Base Composition Statistics.
--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
check uses a lot of memory.
--params : Print the parameter settings.
--quiet : Suppresses the display of errors and summary statistics.
Does not affect the printing of Base Composition Statistics.
=== Optional Space Options for Raw Sequence (Last one specified is used) ===
--autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).
--auto : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).
--baseSpace : ACTGN only
--baseSpace : ACTGN only
--colorSpace : 0123. only
--colorSpace : 0123. only (with 1 character primer base)
=== Usage ===
./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxErrors <numErrors>] [--printableErrors <printableErrors>|--ignoreErrors] [--baseComposition] [--disableSeqIDCheck] [--quiet] [--baseSpace|--colorSpace|--auto] [--params]
=== Examples ===
./fastQValidator --file testFile.txt
./fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 --params
./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors
./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreErrors --disableSeqIDCheck
=== Return Value ===
* 0 - the fastq file is valid.
* < 0 - invalid options specified.
* > 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 ==
When running the fastQValidator Executable, the output starts with a summary of the parameters:
When running the fastQValidator Executable, if the --params option is specified, the output starts with a summary of the parameters:
The following parameters are in effect:
The following parameters are available. Ones with "[]" are in effect:
Input Parameters
Input Parameters
--file [../fastqValidator/test/testFile.txt], --baseComposition,
Space Type : --baseSpace [ON], --colorSpace, --autoDetect
--disableSeqIDCheck, --quiet, --params [ON], --minReadLen [10],
Errors : --ignoreAllErrors, --maxReportedErrors [100]
--maxErrors [-1]
Space Type : --baseSpace, --colorSpace, --auto [ON]
Errors : --ignoreErrors, --printableErrors [20]
The Validator Executable outputs error messages for invalid sequences based on [[FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]].
The Validator Executable outputs error messages for invalid sequences based on [[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.
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.
Base Composition Percentages by Index:
Base Composition Percentages by Index are printed if --printBaseComp is set to ON. For Example:
Base Composition Statistics:
Base Composition Statistics:
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>
Finished processing testFile.txt with 92 lines containing 20 sequences.
Finished processing testFile.txt with 92 lines containing 20 sequences.
There were a total of 17 errors.
There were a total of 17 errors.
== Libraries & Classes ==
== Libraries & Classes ==
*[[FastQFile#Libraries & Classes|libfqf.a]]
*[[C++ Library: libStatGen]]
**ParameterList - Class for reading in Parameters.
*FastQValidator.cpp - Main method for the Executable.
*FastQValidator.cpp - Main method for the Executable.
*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.
*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).
*AutoDetect 64/33 illumina/standard quality scores.
*AutoDetect 64/33 illumina/standard quality scores.
== Discussion ==
== Discussion ==
# The length of read and quality string may be the same or differs by 1 (depending on whether the primer base has a corresponding quality value).
# The length of read and quality string may be the same or differs by 1 (depending on whether the primer base has a corresponding quality value).
#* <span style="color:red">Decided to require a quality score for the primer base.</span>
# Missing values are usually presented by "." or sometimes left as a blank " ".
# Missing values are usually presented by "." or sometimes left as a blank " ".
# Tag names for paired end reads may be the same (e.g. MAQ actually enforces that), and may be in the same file (e.g. BFAST require paired reads in the same file)
# Tag names for paired end reads may be the same (e.g. MAQ actually enforces that), and may be in the same file (e.g. BFAST require paired reads in the same file)
* It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).
* It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).
