jvarkit

AddLinearIndexToBed

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Use a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart.

Usage

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

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

Usage: addlinearindextobed [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ignore
      skip unknown chromosomes.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
  * -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. (use --ignore too 
      prevent error the other chromosomes)
      Default: (chr)?[0-9XY]+
    --version
      print version and exit

Keywords

Creation Date

20140201

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/AddLinearIndexToBed.java

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License

The project is licensed under the MIT license.

Citing

Should you cite addlinearindextobed ? 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

$ cat input.bed | java -jar dist/addlinearindextobed.jar -R  human_g1k_v37.fasta 

10000   1       10000   177417
227417  1       227417  267719
317719  1       317719  471368
(...)
3060255274      Y       23951428        28819361
3095123207      Y       58819361        58917656
3095271502      Y       58967656        59363566
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