Convert
Description
Pad tag by specified number of adjacent bases from the read.
Command help
$ longbow pad --help
Usage: longbow pad [OPTIONS] INPUT_BAM
Pad tag by specified number of adjacent bases from the read.
Options:
-v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG
-t, --threads INTEGER number of threads to use (0 for all) [default:
7]
-o, --output-bam PATH annotated bam output [default: stdout]
-m, --model TEXT The model to use for annotation. If not
specified, it will be autodetected from the BAM
header. If the given value is a pre-configured
model name, then that model will be used.
Otherwise, the given value will be treated as a
file name and Longbow will attempt to read in
the file and create a LibraryModel from it.
Longbow will assume the contents are the
configuration of a LibraryModel as per
LibraryModel.to_json().
-f, --force Force overwrite of the output files if they
exist. [default: False]
-b, --barcode-tag TEXT The barcode tag to adjust
-n, --new-barcode-tag TEXT The barcode tag into which to put the adjusted
value. [default: XM]
-e, --expand INTEGER Expand tag by specified number of bases
--help Show this message and exit.