Segment

$ longbow segment --help
Usage: longbow segment [OPTIONS] INPUT_BAM

  Segment pre-annotated reads from an input BAM file.

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           segment-annotated bam output  [default:
                                  stdout]
  -s, --do-simple-splitting       DEPRECATED.  Do splitting of reads based on
                                  splitter delimiters, rather than whole array
                                  structure. This splitting will cause
                                  delimiter sequences to be repeated in each
                                  read they bound.  This is now the default
                                  setting, and this flag has been DEPRECATED.
  -b, --create-barcode-conf-file  Create a barcode confidence score file based
                                  on the barcodes in the given model.  This
                                  only applies for models that have
                                  annotation_segments where one such segment
                                  is annotated into the raw barcode field (CR)
  -m, --model TEXT                The model to use for annotation.  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().  [default: mas15]
  -r, --require-cbc-and-umi       Passing reads must have CBC and UMI.
                                  [default: False]
  --help                          Show this message and exit.

$ longbow segment -o segmented.bam annotated.bam
[INFO 2021-08-12 09:57:45  segment] Invoked via: longbow segment -o segmented.bam annotated.bam
[INFO 2021-08-12 09:57:45  segment] Running with 11 worker subprocess(es)
[INFO 2021-08-12 09:57:45  segment] Using bounded region splitting mode.
[INFO 2021-08-12 09:57:48  segment] Using The standard MAS-seq 15 array element model.
[INFO 2021-08-12 09:57:50  segment] Segmented 8 reads with 113 total segments.
[INFO 2021-08-12 09:57:50  segment] Done. Elapsed time: 4.84s.