refFromAlns {CrispRVariants} | R Documentation

## refFromAlns

### Description

Reconstruct the reference sequence from alignments reads using the CIGAR

### Usage

    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

[Package CrispRVariants version 1.14.0 Index]