Convert
Description
Guess the best pre-built array model to use for annotation.
Command help
$ longbow peek --help
Usage: longbow peek [OPTIONS] INPUT_BAM
Guess the best pre-built array model to use for annotation.
Options:
-v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or
DEBUG
-p, --pbi PATH BAM .pbi index file
-t, --threads INTEGER number of threads to use (0 for all)
[default: 7]
-o, --output-model PATH model name output [default: stdout]
-c, --chunk TEXT Process a single chunk of data (e.g. specify
'2/4' to process the second of four equally-
sized chunks across the dataset)
-n, --num-reads INTEGER Number of reads to examine when trying to
guess the array model
-l, --min-length INTEGER Minimum length of a read to process. Reads
shorter than this length will not be
annotated. [default: 0]
-L, --max-length INTEGER Maximum length of a read to process. Reads
longer than this length will not be
annotated. [default: 30000]
--min-rq FLOAT Minimum ccs-determined read quality for a
read to be annotated. CCS read quality
range is [-1,1]. [default: -2.0]
-f, --force Force overwrite of the output files if they
exist. [default: False]
-d, --include-deprecated-models
Examine the deprecated built-in models as
well [default: False]
--help Show this message and exit.