SetFileCluster

Last commit

Cluster records of setfiles into files containing a sum to basepaires close to 'x' bp

Usage

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

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

Usage: setfilecluster [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -J, --jobs
      number of clusters. (or specify --size)
      Default: -1
    -o, --out
      Output file. Optional . Default: stdout. For action=cluster, output is: 
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -S, --size
      number of bases max per bin. (or specify --jobs). A distance specified 
      as a positive integer.Commas are removed. The following suffixes are 
      interpreted : b,bp,k,kb,m,mb,g,gb
      Default: -1
    -t, --trim-chr
      Remove chr prefix in chromosome names on output.
      Default: false
    --version
      print version and exit

Keywords

setfile
bed

Creation Date

20210125

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/setfile/SetFileCluster.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 setfilecluster ? 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

TODO