jvarkit

SwingVcfJexlFilter

Filter VCF using Java Swing UI and JEXL/Javascript expression

Usage

Usage: java -jar dist/swingvcfjexl.jar  [options] Files
Usage: swingvcfjexl [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit

Keywords

• vcf
• visualization
• swing
• jexl
• javascript

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 swingvcfjexl

The java jar file will be installed in the dist directory.

Creation Date

20220413

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/SwingVcfJexlFilter.java

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 swingvcfjexl ? 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

Example

java -jar dist/swingvcfjexl.jar src/test/resources/rotavirus_rf.vcf.gz

Screenshot

https://twitter.com/yokofakun/status/1514287386410336259

This site is open source. Improve this page.