Python callbacks

Bedder embeds Python to compute custom columns and filters while the CLI processes intervals. Pass a callback file with --python and select a function with -c 'py:name':

https://quinlan-lab.github.io/bedder-rs/

To use bedder as a Rust library, run Python inside a Rust application, or expose your project as a Python module, see Embedding.

def bedder_n_overlapping(fragment) -> int:
    """Number of reported B intervals."""
    return len(fragment.b)

bedder intersect \
  -a a.bed -b b.bed -g reference.fa.fai \
  --python callbacks.py -c 'py:n_overlapping'

Callback names must start with bedder_, but the command-line selector omits that prefix. Every discovered callback must have a concrete return annotation of int, float, str, or bool and must return exactly that type. Do not use postponed annotations (from __future__ import annotations) or prefix helper functions with bedder_.

Intersection callbacks receive a report fragment. fragment.a is the query position, fragment.b is the list of reported matching positions, and fragment.id is the fragment identifier. Positions expose chrom, start, and stop; use .bed() for BED-specific fields or .vcf() for VCF/BCF-specific fields.

The callback file is loaded by Bedder's embedded interpreter. It is not a normal standalone program, and it should not import bedder at module load time.

See Use Bedder from an agent for the complete callback object model, VCF examples, map callback contracts, validation workflow, and common failure modes.

The generated Rust/Python API documentation is also available at quinlan-lab.github.io/bedder-rs.