VCFShuffle

##Motivation

Shuffle a VC

##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 vcfshuffle

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 vcfshuffle 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/vcfshuffle.jar  [options] (stdin|file.vcf|file.vcf.gz)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-maxRecordsInRam|--maxRecordsInRam (NUMBER) When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort a SAM/VCF/... file, and increases the amount of RAM needed. Default value : "500000".
-tmpdir|--tmpdir (TMPDIR) Set temporary directory
-N|--seed (VALUE) random seed. Optional. -1 = time. Default value : "-1L".
-h|--help print help
-version|--version show version and exit

##Source Code