BedToXml

Convert BED to XML

Usage

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

Usage: java -jar dist/jvarkit.jar bed2xml  [options] Files

Usage: bed2xml [options] Files
  Options:
    --columns
      Optional Comma separated list names of column starting from the 3rd 
      column (after 'end'). Use '.' to ignore.
      Default: <empty string>
    --dict-out
      Save reduced/modified dict to this file
    -d, --distance
      if >=0, add a 'y' attribute that could be used to display the bed 
      records in a browser,     this 'y' is the graphical row where the item 
      should be displayed.  This distance is the distance between two item 
      where there is a collision. Memory consuming . 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
    --first-line-header
      First line is a header. Use it as the name of the columns
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --min-contig-length
      keep chromosomes which length is greater than 'x'
      Default: 0
    --omit-xml-desclaration
      Don't print XM declaration.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
    --regex
      keep chromosomes matching that regular expression
    --type
      BedType. bedGraph will print the min/max of value. bed12 will display 
      each block
      Default: generic
      Possible Values: [generic, bedGraph, bed12]
    --version
      print version and exit

Keywords

• bed
• xml

Creation Date

20251128

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bed2xml/BedToXml.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bed2xml/BedToXmlTest.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 bed2xml ? 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