jvarkit

Biostar105754

bigwig : peak distance from specific genomic region

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar105754  [options] Files

Usage: biostar105754 [options] Files
  Options:
  * -B, --bigwig
      Big Wig file
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• wig
• bigwig

See also in Biostars

• https://www.biostars.org/p/105754

Creation Date

20140708

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar105754.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar105754Test.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 biostar105754 ? 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

$  echo -e "1\t1000\t20000\n3\t100\t200\nUn\t10\t11"  |\
  java -jar dist/biostar105754.jar -B path/to//All_hg19_RS_noprefix.b


#no data found for	Un	10	11
1	1000	1001	0.0	1	1000	20000
3	100	101	0.0	3	100	200

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