BedStats

Last commit

statistics about one or more file

Usage

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

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

Usage: bedstats [options] Files
  Options:
    --disable-normalize-contig
      do not normalize contig name '1'->'chr1'
      Default: false
    -f, --fraction
      for overlap between to BED file. Two BED record overlap if they  both 
      share 'x' fraction of overlap compared to their lengthA decimal number 
      between 0.0 and 1.0. If the value ends with '%' it is interpretted as a 
      percentage eg. '1%' => '0.01'. A slash '/' is interpretted as a ratio. 
      e.g: '1/100' => '0.01'.
      Default: 1.0E-9
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -o, --out
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --version
      print version and exit

Keywords

  • bed
  • stats
  • multiqc

Creation Date

20260130

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bedstats/BedStats.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bedstats/BedStatsTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite bedstats ? 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

input is bed on standard input or it's a set of interval files (.bed, .interval_list, .gtf, etc... )

output is text file containing multiple chuncks for multiqc

Example

$ java -jar dist/bedstats.jar < in1.bed > out.txt
$ java -jar dist/bedstats.jar in1.bed in2.bed in3.bed > out.txt