gappedref: gappedRef

In HLindsay/AlignmentTools: Common operations on GenomicAlignments

Description

Given a set of sequences aligned to a reference, introduce gaps in the reference sequence corresponding to insertion locations in the aligned sequences. TO DO: HOW ARE AMBIGUOUS ALIGNMENTS TREATED?

Usage

gappedRef(reference, alignments, ...)

## S4 method for signature 'DNAString,GAlignments'
gappedRef(reference, alignments, ...)

Arguments

reference	Ungapped reference sequence
alignments	Sequences aligned to the reference sequence
...	Extra arguments

Author(s)

Helen Lindsay

HLindsay/AlignmentTools documentation built on May 8, 2019, 1:36 a.m.