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[[Category:Software|FastQValidator]]
[[Category:C++|Software|FastQValidator]]
== Status ==
= fastQValidator Overview =
The initial version of a FASTQ Validator is complete. It was built using the [[FastQFile]] class which is part of the [[C++ Library: libStatGen|StatGen Library]].
The fastQValidator validates the format of fastq files.
The initial version of a FASTQ Validator is complete. It was built using the [[FastQFile]] class 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
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 '''coming soon'''
* 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 ===
Release downloads are '''Coming Soon'''.
=== 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.
== Valid FastQ File Requirements ==
== Valid FastQ File Requirements ==
