jvarkit

SamFindClippedRegions

Last commit

Usage

Usage: samfindclippedregions [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
    -B
      bed file
    -c
      min size of clipped read
      Default: 20

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew samfindclippedregions

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/SamFindClippedRegions.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite samfindclippedregions ? 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