refFromAlns: refFromAlns

Description Usage Arguments Value Author(s)

Description

Reconstruct the reference sequence from alignments reads using the CIGAR

Usage

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refFromAlns(alns, location, ...)

## S4 method for signature 'GAlignments,ANY'
refFromAlns(alns, location, ...,
  keep.names = FALSE)

## S4 method for signature 'GAlignments,GRanges'
refFromAlns(alns, location, ...)

Arguments

alns

Alignments to use for inferring the reference sequence

location

The location to infer the reference for.

...

additional arguments

keep.names

Should read names be added to the result if present? (Default: FALSE)

Value

The reference sequences corresponding to the provided alignments

A DNAStringSet (signature = c("GAlignments", "ANY"))

A DNAString (signature = c("GAlignments", "GRanges"))

Author(s)

Helen Lindsay


HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.