ForkVcf

##Motivation

Fork a VCF.

##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)
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

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

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 forkvcf 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/forkvcf.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
-g|--groupfile (GROUP) Chromosome group file. Intervals are 1-based. If undefined, splitvcf will use the sequence dictionary to output one vcf per contig.
-n|--count (VALUE) number of vcf files to generate Default value : "2".
-c|--splitbychunk When this option is used, the variant are first saved in a temporary file, the number of variant is dividided by 'count' and the output files are lineray produced. The default is to dispatch the variants as they are coming in the stream. Default value : "false".
-m|--manifest (VALUE) optional save produced vcf filenames in this file.
-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/misc/ForkVcf.java

Output

Output filename (option -o) MUST contain the word GROUPID.

Example

cat input.vcf | java -jar dist/forkvcf.jar -n 3 -o "_tmp.GROUPID.vcf" [main] INFO jvarkit - opening VCF file "_tmp.00001.vcf" for writing [main] INFO jvarkit - opening VCF file "_tmp.00002.vcf" for writing [main] INFO jvarkit - opening VCF file "_tmp.00003.vcf" for writing

$ wc _tmp.0000* 226 6819 143947 _tmp.00001.vcf 226 6819 140792 _tmp.00002.vcf 225 6161 125219 _tmp.00003.vcf