liftOverLax: Like 'rtracklayer::liftOver()' but "fills in" small gaps.

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

Like rtracklayer::liftOver() but "fills in" small gaps.

Description

This is identical to rtracklayer::liftOver(), except that gaps smaller than a specified size will be filled in. This allows the liftover process to tolerate small indels in the old genome relative to the new one without breaking up contiguous regions.

Usage

liftOverLax(x, chain, ..., allow.gap = 0)

Arguments

x, chain, ...	These arguments have the same meaning as in rtracklayer::liftOver().
allow.gap	Maximum gap size to "fill in". If set to zero, this is equivalent to rtracklayer::liftOver().

Details

Obviously this is kind of an ugly hack.

Value

See rtracklayer::liftOver().

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.