cigarFromMSA: CIGAR from Multiple Sequence Alignment

In HLindsay/AlignmentTools: Common operations on GenomicAlignments

Description

Construct a CIGAR string from a multiple sequence alignment

Usage

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

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.