jvarkit

BedToHilbert

BED to hilbert curve as SVG.

Usage

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

Usage: java -jar dist/jvarkit.jar bed2hilbert  [options] Files

Usage: bed2hilbert [options] Files
  Options:
    --columns
      Optional Comma separated list names of column starting from the 3rd 
      column (after 'end'). Use '.' to ignore.
      Default: <empty string>
    --css
      load custom CSS style file
    --first-line-header
      The first line of the bed file is a header
      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, --recursion
      Hilbert Curve level of recursion
      Default: 6
  * -R, --reference, --dict
      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
    --version
      print version and exit
    -w, --width
      Image width
      Default: 1000

Keywords

• bed
• xml
• svg
• hilbert

Creation Date

20260417

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bed2hilbert/BedToHilbert.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bed2hilbert/BedToHilbertTest.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 bed2hilbert ? 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

Motivation

Creates a Hilbert SVG Graph for a BED file.

Example

 java -jar dist/jvarkit.jar bed2hilbert  -R src/test/resources/rotavirus_rf.dict input.bed > out.svg

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