BamUtil

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
  • See 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 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.

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 bamUtil_1.0.0 directory and type make all.

BamUtilLibStatGen.1.0.0.tgz‎ - Released 10/10/2011

BamUtilLibStatGen.1.0.0 Release Notes

• Initial release of bamUtil that includes libStatGen version 1.0.0. It started from the tool found in the deprecated StatGen repository.
• Contains: libStatGen version 1.0.0 validate, convert, dumpHeader, splitChromosome, writeRegion, dumpRefInfo, dumpIndex, readIndexedBam, filter, readReference, revert, diff, squeeze, findCigars, stats.

Release of just BamUtil (does not include libStatGen)

To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_1.0.0 directory and type make all.

BamUtil.1.0.0.tgz‎ - Released 10/10/2011

BamUtilLibStatGen.1.0.0 Release Notes

• Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.
• Contains: libStatGen version 1.0.0 validate, convert, dumpHeader, splitChromosome, writeRegion, dumpRefInfo, dumpIndex, readIndexedBam, filter, readReference, revert, diff, squeeze, findCigars, stats.

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.

• Rewrite SAM/BAM Files
  • convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)
  • writeRegion - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name
  • splitChromosome - Split BAM by Chromosome
  • splitBam - Split SAM/BAM file by Read Group
  • findCigars - Output just the reads that contain any of the specified CIGAR operations

• Modify & write SAM/BAM Files
  • clipOverlap - Clip overlapping read pairs so they do not overlap
  • filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high
  • revert - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
  • squeeze - Reduce file size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers

• Informational Tools
  • validate - Read and Validate a SAM/BAM file
  • diff - Print the diffs between 2 bams
  • stats - Print some basic statistics on a SAM/BAM file
  • gapInfo - Print information on the gap between read pairs in a SAM/BAM file

• Print Information in Readable Form:
  • dumpHeader - Print SAM/BAM header
  • dumpRefInfo - Print SAM/BAM Reference Information
  • dumpIndex - Dump a BAM index file into an easy to read text version
  • readReference - Print the reference string for the specified region

• Dummy/Example Tools:
  • readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file

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

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