bedder (tools)

This is an early release of the library for feedback, especially from rust practitioners.

Documentation

Please find documentation here.

Problem statement

BEDTools is extremely useful but adding features and maintaining existing ones is a challenge. We want a library (in bedder) that is:

1. flexible enough to support most use-cases in BEDTools
2. fast enough
3. extensible so that we don't need a custom tool for every possible use-case.

Solution

To do this, we provide the machinery to intersect common genomics file formats (and more can be added by implementing a simple trait) and we allow the user to write python functions that then write columns to the output. As a silly example, the user may want to count overlaps but only if the start position of the overlapping interval is even; that could be done with this expression:

def bedder_odd(fragment) -> int:
    """return odd if the start of the query interval is odd. otherwise even"""
    return sum(1 for _ in fragment.b if b.start % 2 == 0)

There are several things to note here:

• The function name must start with bedder_ what follows that will be used as the name in the command-line and as the output e.g. in the VCF INFO field.
• The function must have a return type annotation (int, str, float, bool are supported)
• The docstring will be used as the description for VCF output, if appropriate
• The function must accept a fragment--that is, a piece of an alignment.

This function, if placed in a file named example.py could be used as:

bedder -a some.bed -b other.bed -P example.py -c 'py:odd`

where odd matches the function name above after dropping the bedder_ prefix.