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BedAnnotateFromBed tool help

BedAnnotateFromBed (2020_03-137-gb82c85b1)

Annotates BED file regions with information from a second BED file.

Mandatory parameters:
  -in2 <file>     BED file that is used as annotation source.

Optional parameters:
  -in <file>      Input BED file. If unset, reads from STDIN.
                  Default value: ''
  -out <file>     Output BED file. If unset, writes to STDOUT.
                  Default value: ''
  -col <int>      Annotation source column (if column number does not exist, 'yes' is used).
                  Default value: '4'
  -clear          Clear all annotations present in the 'in' file.
                  Default value: 'false'
  -no_duplicates  Remove duplicate annotations if several intervals from 'in2' overlap.
                  Default value: 'false'
  -overlap        Annotate overlap with regions in 'in2'. The regular annotation is appended in brackets.
                  Default value: 'false'
  -url_decode     Decode URL encoded characters
                  Default value: 'false'
  -name <string>  Use this name as column header of TSV files output files. If unset, the base file name if 'in2' is used.
                  Default value: ''

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'.

BedAnnotateFromBed changelog

BedAnnotateFromBed 2020_03-137-gb82c85b1

2020-05-19 Added parameter 'name'.
2019-07-09 Added parameters 'col', 'overlap' and 'no_duplicates'; Fixed 'clear' parameter.
2017-11-28 Added 'clear' flag.
2017-11-03 Initial commit.

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