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BedpeAnnotateFromBed tool help

BedpeAnnotateFromBed (2021_12-170-g1acf8802)

Annotates a BEDPE file with information from a BED file.

Mandatory parameters:
  -bed <file>          BED file that is used as annotation source.

Optional parameters:
  -in <file>           Input BEDPE file. If unset, reads from STDIN.
                       Default value: ''
  -out <file>          Output BEDPE file. If unset, writes to STDOUT.
                       Default value: ''
  -col <int>           Annotation source column (default: 4).
                       Default value: '4'
  -col_name <string>   Name of the annotated column
                       Default value: 'ANNOTATION'
  -no_duplicates       Remove duplicate annotations if several intervals from 'bed' overlap.
                       Default value: 'false'
  -url_decode          Decode URL encoded characters.
                       Default value: 'false'
  -replace_underscore  Replaces underscores with spaces in the annotation column.
                       Default value: 'false'
  -max_value           Select maximum value if several intervals from 'bed' overlap. (only for numeric columns)
                       Default value: 'false'
  -only_breakpoints    Only annotate overlaps with the confidence intervall of the break points.
                       Default value: 'false'

Special parameters:
  --help               Shows this help and exits.
  --version            Prints version and exits.
  --changelog          Prints changeloge and exits.
  --tdx                Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

BedpeAnnotateFromBed changelog

BedpeAnnotateFromBed 2021_12-170-g1acf8802

2022-02-17 Added 'max_value' parameter.
2020-01-27 Initial commit.

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