align2cigar

R2026b

Convert aligned sequences to corresponding signatures in CIGAR format

Syntax

Cigars = align2cigar(Alignment,Ref)

[Cigars,Starts] = align2cigar(Alignment,Ref)

Description

Cigars = align2cigar(Alignment,Ref) converts aligned sequences represented in Alignment into Cigars using the reference sequence specified by Ref.

[Cigars,Starts] = align2cigar(Alignment,Ref) also returns Starts, a vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.

Examples

Convert aligned sequences to CIGAR strings

This example shows how to convert aligned strings to CIGAR strings

Create a cell array of aligned strings, create a string specifying a reference sequence, and then convert the alignment to CIGAR strings:

aln = ['ACG-ATGC'; 'ACGT-TGC'; '  GTAT-C']

aln = 3×8 char array
    'ACG-ATGC'
    'ACGT-TGC'
    '  GTAT-C'

ref =  'ACGTATGC';
[cigar, start] = align2cigar(aln, ref)

cigar = 1×3 cell
    {'3=1D4='}    {'4=1D3='}    {'4=1D1='}

start = 1×3

     1     1     3

Input Arguments

Alignment — Aligned sequence

cell array of aligned character vectors | string vector | character array

Aligned sequence, specified as a cell array of aligned character vectors, a string vector, or a character array. Soft clippings are assumed to be represented by lowercase letters in the aligned sequences. Skipped positions are assumed to be represented by a period . in the aligned sequences.

Data Types: char | string | cell

Ref — Aligned reference sequence

character vector | string

Aligned reference sequence, specified as a character vector or string. The length of Ref must equal the number of columns in Alignment.

Data Types: char | string

Output Arguments

Cigars — Converted sequence in CIGAR format

cell array of character vectors

Converted sequence in CIGAR format, returned as a cell array of character vectors. Each entry in Cigars corresponds to one entry in Alignment.

Starts — Start position of each aligned sequence

integer vector

Start position of each aligned sequence, returned as an integer vector. The start positions are with respect to the ungapped reference sequence specified by Ref.

Version History

Introduced in R2010b