Difference between revisions of "BamUtil"

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== Where to Find It ==
 
== Where to Find It ==
The bamUtil repository is available both via release downloads (coming soon) and via github.
+
{{ToolGitRepo|repoName=bamUtil|exe=bam}}
 
 
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.
 
 
 
If you download from github or use git to keep up to date, you also need to download our library: [[C++ Library: libStatGen|libStatGen]].
 
 
 
The releases will be available both with and without libStatGen included.  If you download the verison without libStatGen included, you will also need to download libStatGen separately.
 
(It will be available without libStatGen in case you already have a downloaded version of libStatGen that you want to use.
 
 
 
=== 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/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 <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.
 
 
 
 
 
  
 
= Programs =
 
= Programs =

Revision as of 10:30, 9 September 2011


bamUtil Overview

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, bam.


Where to Find It

The bamUtil repository is available both via release downloads and via github.

On github, https://github.com/statgen/bamUtil, you can both browse and download the bamUtil source code as well as explore the history of changes.

You can obtain the source either with or without git.

The releases may be available both with and without libStatGen included.

If you do not use the release version that already contains libStatGen, you need to download the library: libStatGen.

If you try to compile bamUtil and it cannot find libStatGen, it will fail and provide instructions of what to do next:

  • if libStatGen is in a different location then expected
    • follow the directions to set the path to libStatGen
  • if libStatGen is not downloaded and you have git
    • make libStatGen will download via git and build libStatGen
  • if libStatGen is not downloaded and you don't have git

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 bamUtil in the current directory.

Then just cd bamUtil and compile.

Get the latest Updates (update your copy)

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

  1. cd pathToYourCopy/bamUtil
  2. make clean
  3. git pull
  4. make all

Git Refresher

If you decide to use git, but need a refresher, see How To Use Git or Notes on how to use git (if you have access)


Downloading From GitHub Without Git

If you download the latest code/version, make sure you periodically update it by downloading a newer version.

From github you can download:

  1. Latest Code (master branch)
    via Website
    1. Goto: https://github.com/statgen/bamUtil
    2. Click on the Download ZIP button on the right side panel.
    via Command Line
    wget https://github.com/statgen/bamUtil/archive/master.tar.gz
    or
    wget https://github.com/statgen/bamUtil/archive/master.zip
  2. Specific Release (via a tag)
    via Website
    1. Goto: https://github.com/statgen/bamUtil/releases to see the available releases
    2. Click zip or tar.gz for the desired version.
    via Command Line
    wget https://github.com/statgen/bamUtil/archive/<tagName>.tar.gz
    or
    wget https://github.com/statgen/bamUtil/archive/<tagName>.zip


After downloading the file, uncompress (unzip/untar) it. The directory created will be named bamUtil-<name of version you downloaded>.

Building

After obtaining the bamUtil repository (either by download or from github), compile the code using:

make all  

Object (.o) files are compiled into the obj directory with a subdirectory debug and profile for the debugging and profiling objects.

This creates the executable(s) in the bamUtil/bin/ directory, the debug executable(s) in the bamUtil/bin/debug/ directory, and the profiling executable(s) in the bamUtil/bin/profile/ directory.

make install installs the opt binary if you have permission.

make test compiles for opt, debug, and profile and runs the tests (found in the test subdirectory).

To see all make options, type make help.


If compilation fails due to warnings being treated as errors, please contact us so we can fix the warnings. As a work-around to get it to compile, you can disable the treatment of warnings as errors by editing libStatGen/general/Makefile to remove -Werror.

Programs

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 bam executable has the following functions.



This executable is built using C++ Library: libStatGen.

Just running ./bam will print the Usage information for the bam executable.