BamTreePack

##Motivation

Create a TreeMap from one or more SAM/BAM file. Ouput is a SVG file.

##Compilation

Requirements / Dependencies

java 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
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

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

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 addinging standalone=yes on the command line:

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

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

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

##Synopsis

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

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-c|--config (CONFIG.XML) XML config file
-x|--dimension (VALUE) dimension of the output rectangle Default value : "1000x1000".
-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/treepack/BamTreePack.java

Synopsis

$ $ java -jar dist/bamtreemap.jar -c config.xml (stdin|bam1 bam2 ....) > out.svg

XML config

XML root is . children is '' . A '' has an attribute 'name'. The text content of the will be evaluated as a javascript expression with the embedded javascript engine. The javascript engine injects record a https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/SAMRecord.java and header a https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html.

Example

$ cat config.xml

<?xml version="1.0"?>
<treepack>
  <node name="chr">(record.getReadUnmappedFlag()?"UNMAPPED":record.getContig())</node>
  <node name="mapq">(record.getReadUnmappedFlag()?null:record.getMappingQuality())</node>
</treepack>

$ java  -jar dist/bamtreepack.jar -c config.xml  \
  "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/NA12340/alignment/NA12340.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.bam" \
  "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/NA12273/alignment/NA12273.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.bam" > out.svg