cigarFromMSA: CIGAR from Multiple Sequence Alignment

Description Usage Arguments Author(s) Examples

Description

Construct a CIGAR string from a multiple sequence alignment

Usage

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cigarFromMSA(aln, ...)

## S4 method for signature 'MsaDNAMultipleAlignment'
cigarFromMSA(aln, ..., ref = NULL)

## S4 method for signature 'DNAStringSet'
cigarFromMSA(aln, ..., ref = NULL)

Arguments

aln

A multiple sequence alignment

...

Extra arguments

ref

character(1) Name of sequence in aln to use as a reference (Default: NULL)

ref

character(1) name of the alignment in alns to use as a reference (Default: NULL)

Author(s)

Helen Lindsay

Examples

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aln <- DNAStringSet(c("AA--CC","AATTCC","AATTC-"))
names(aln) <- c("A","B","C")
cigarFromMSA(aln)
cigarFromMSA(aln, ref = "A")
cigarFromMSA(aln, ref = "B")
cigarFromMSA(aln, ref = "C")

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