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[[Category:BAM Software]]
[[Category:BAM Software]]
= bam Executable =
= bamUtil =
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, <code>bam</code>.
== Where to Find It ==
The bamUtil repository is available both via release downloads (coming soon) 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.
You can access the latest version with or without git.
=== Using github ===
If you download from github or use git to keep up to date, you also need <code>libStatGen</code>. [[http://genome.sph.umich.edu/wiki/C%2B%2B_Library:_libStatGen|Get libStatGen]].
==== 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/bamUtil.git
or
git clone git://github.com/statgen/bamUtil.git
Either of these commands create a directory called <code>bamUtil</code> in the current directory.
Then just <code>cd bamUtil</code> and [[BamUtil#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/bamUtil</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/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.
== 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 bamUtil/bin/ directory.
On github, you can both browse and download the latest version of the library, as well as explore the history of changes.
You can access the latest version with or without using git.
[edit]
The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
