BamStats02View

##Motivation

Statistics about the flags and reads in a BAM. Visualize date from BamStats02

##Compilation

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

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make bamstats02view

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 bamstats02view standalone=yes

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

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/bamstats02view.jar  [options] (stdin|file)

Options

##Source Code

Explore those statistics with a graphical user interface. Left-click shows a popup menu used to include/exclude categories.

$java -jar dist/bamstats02view.jar output_of_bamstats02.tsv

$java -jar dist/bamstats02view.jar output.tsv

The project is licensed under the MIT license.

The current reference is:

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