Changes

The bamUtil repository is available both via release downloads (coming soon) and via github.

The {{{repoName}}} repository is available both via release downloads and via github.

On github, you can both browse and download the latest version of the repository as well as explore the history of changes.

On github, you can both browse and download the latest version of the repository as well as explore the history of changes.

===== Clone (get your own copy) =====

===== Clone (get your own copy) =====

You can create your own git clone (copy) using:

You can create your own git clone (copy) using:

  git clone https://github.com/statgen/bamUtil.git

  git clone https://github.com/statgen/{{{repoName}}}.git

or

or

  git clone git://github.com/statgen/bamUtil.git

  git clone git://github.com/statgen/{{{repoName}}}.git

Either of these commands create a directory called <code>bamUtil</code> in the current directory.

Either of these commands create a directory called <code>{{{repoName}}}</code> in the current directory.

Then just <code>cd bamUtil</code> and [[BamUtil#Building|compile]].

Then just <code>cd {{{repoName}}}</code> and [[#Building|compile]].

===== Get the latest Updates (update your copy) =====

===== Get the latest Updates (update your copy) =====

To update your copy to the latest version (a major advantage of using git):

To update your copy to the latest version (a major advantage of using git):

# <code>cd pathToYourCopy/bamUtil</code>

# <code>cd pathToYourCopy/{{{repoName}}}</code>

# <code>make clean</code>

# <code>make clean</code>

# <code>git pull</code>

# <code>git pull</code>

Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/bamUtil/archives/master.

Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/bamUtil/archives/master.

The downloaded tar file is named "statgen-bamUtil-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 bamUtil, 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.

The downloaded tar file is named "statgen-{{{repoName}}}-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 {{{repoName}}}, 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 ==

== Building ==

After obtaining the bamUtil repository (either by download or from github), compile the code using <code>make all</code>.  This creates the executable, <code>bam</code>, in the <code>bamUtil/bin/</code> directory, the debug executable in the <code>bamUtil/bin/debug/</code> directory, and the profiling executable in the <code>bamUtil/bin/profile/</code> directory.

After obtaining the {{{repoName}}} repository (either by download or from github), compile the code using <code>make all</code>.  This creates the executable, <code>{{{exe|{{{repoName}}}}}}</code>, in the <code>{{{repoName}}}/bin/</code> directory, the debug executable in the <code>{{{repoName}}}/bin/debug/</code> directory, and the profiling executable in the <code>{{{repoName}}}/bin/profile/</code> directory.