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Bedder - simple, flexible intersections

bedder is organized into subcommands for easier usage:

bedder v0.1.6

Usage: bedder <COMMAND>

Commands:
  full       Full functionality with all options (almost never use this)
  intersect  Intersection mode - hides closest options
  closest    Closest mode - hides overlap requirements
  help       Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help

Subcommands

  • bedder intersect - For finding overlaps between intervals. This is the most commonly used mode and hides closest-related options for simplicity.
  • bedder closest - For finding the nearest intervals. This mode hides overlap requirement options.
  • bedder full - Contains all options from both intersect and closest modes. Use this only when you need access to all features simultaneously.

Common Options (for all subcommands)

All subcommands share common options:

  • -a <QUERY_PATH> - input file
  • -b <OTHER_PATHS> - other file
  • -g, --genome <GENOME_FILE> - genome file for chromosome ordering
  • -c, --columns <COLUMNS> - columns to output (format: name:type:description:number:value_parser)
  • -o, --output <OUTPUT_PATH> - output file (default: stdout)
  • -p, --a-piece <A_PIECE> - the piece of the a intervals to report [default: whole] [possible values: none, piece, whole, inverse]
  • -P, --b-piece <B_PIECE> - the piece of the b intervals to report [default: whole] [possible values: none, piece, whole, inverse]
  • --python <PYTHON_FILE> - python file with functions to be used in columns
  • -f, --filter <FILTER> - optional filter expression (Python boolean expression; 'r' and 'fragment' are the current report fragment) indicates if the fragment should be included in the output

Intersect-specific Options

  • -m, --a-mode <INTERSECTION_MODE> - intersection mode for a-file [default: default] [possible values: default, not, piece]
  • -M, --b-mode <B_MODE> - intersection mode for b-file [default: default] [possible values: default, not, piece]
  • -r, --a-requirements <A_REQUIREMENTS> - a-requirements for overlap (float < 1, percentage, or integer for bases)
  • -R, --b-requirements <B_REQUIREMENTS> - b-requirements for overlap (float < 1, percentage, or integer for bases)

Closest-specific Options

  • -n, --n-closest <N_CLOSEST> - report the n-closest intervals
  • -d, --max-distance <MAX_DISTANCE> - maximum distance to search for closest intervals

Logging

bedder has logging for debugging and tracing. The default is to only show warnings. If interested in more granular (verbose) output, set an environment variable:

export RUST_LOG=info

sometimes this can be helpful if bedder isn't behaving how you expect.