Bam2Raster

##Motivation

BAM to raster graphics

##Compilation

Requirements / Dependencies

Since 2016-05-30 the compilation of the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk) library requires gradle http://gradle.org.

• java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
• GNU Make >= 3.81
• curl/wget
• git
• gradle http://gradle.org is only required to compile the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk). And I think htsjdk installs it.
• xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make bam2raster

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by adding standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make bam2raster standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

to set the gradle user home ( https://docs.gradle.org/current/userguide/build_environment.html#sec:gradle_properties_and_system_properties )

gradle.user.home=/dir1/dir2/gradle_user_home

##Synopsis

$ java -jar dist/bam2raster.jar  [options] (stdin|file) 

Options

• -o|--output (OUTPUT-FILE) Output file. Default:stdout.
• -b|--bases print bases Default value : "false".
• -r|--region (CHR:START-END) restrict to that region. REQUIRED
• -R|--reference (file.fa) indexed fasta reference
• -w|--width (IMAGE-WIDTH) indexed fasta reference
• -N|--name print read name Default value : "false".
• -printBases|--printBases do not print Bases Default value : "false".
• -h|--help print help
• -version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/Bam2Raster.java

Example

java -jar dist/bam2raster.jar \
	-o ~/jeter.png \
        -r 2:17379500-17379550 \
        -R  human_g1k_v37.fasta \
        sample.bam

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite bam2raster ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030