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 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.