jvarkit
VcfToZip
Reads a stream of concatenated VCFs and insert them into a Zip file
Usage
Usage: vcf2zip [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output zip file.
-p, --prefix
Prefix all zip entries with this prefix
Default: VCF
-t, --title
Try to find ##(TITLE)=abcdefghijk in the VCF header and use it as the
name of the inserted VCF file
Default: <empty string>
--version
print version and exit
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2zip
The java jar file will be installed in the dist directory.
Source code
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 vcf2zip ? 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
Motivation
This tool was used to create a zip from the output of VCFburdensplitter which is a stream of VCFs.
Example
$ cat ~/input.vcf ~/input.vcf ~/input.vcf | java -jar dist/vcf2zip.jar -o jeter.zip
[main] INFO jvarkit - Command Line args : -o jeter.zip
[main] INFO jvarkit - Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27
[main] INFO jvarkit - reading concatenated vcf from stdin
[main] INFO jvarkit - VCF/vcf2zip.00001.vcf
[main] INFO jvarkit - Count: 499 Elapsed: 10 seconds(0.05%) Remains: 6 hours(99.95%) Last: 1:1431105
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - VCF/vcf2zip.00002.vcf
[main] INFO jvarkit - Count: 530 Elapsed: 10 seconds(0.05%) Remains: 5 hours(99.95%) Last: 1:1510577
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - VCF/vcf2zip.00003.vcf
[main] INFO jvarkit - Count: 530 Elapsed: 10 seconds(0.05%) Remains: 5 hours(99.95%) Last: 1:1510577
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - done. Number of VCFs:3
[main] INFO jvarkit - End JOB [Mon May 02 12:30:24 CEST 2016] VcfToZip done. Elapsed time: 0.85 minutes.
$ unzip -t jeter.zip
Archive: jeter.zip
testing: VCF/vcf2zip.00001.vcf OK
testing: VCF/vcf2zip.00002.vcf OK
testing: VCF/vcf2zip.00003.vcf OK
No errors detected in compressed data of jeter.zip.