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align2cigar

Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format

Syntax

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

Description

[Cigars,Starts] = align2cigar(Alignment,Ref) converts aligned sequences represented in Alignment, a cell array of aligned character vectors or a character array, into Cigars, a cell array of corresponding CIGAR–formatted character vectors, using the reference sequence specified by Ref, a character vector. It also returns Starts, a vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.

Input Arguments

Alignment

Cell array of character vector or a character array representing aligned sequences. Soft clippings are assumed to be represented by lowercase letters in the aligned sequences. Skipped positions are assumed to be represented by . in the aligned sequences.

Ref

Character vector specifying an aligned reference sequence. The length of Ref must equal the number of columns in Alignment.

Output Arguments

Cigars

Cell array of CIGAR-formatted character vectors corresponding to each aligned sequence in Alignment.

Starts

Vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.

Examples

collapse all

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 =

ACG-ATGC
ACGT-TGC
  GTAT-C

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

  1×3 cell array

    '3M1D4M'    '4M1D3M'    '4M1D1M'


start =

     1     1     3

References

[1] Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Goncalo, A., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 16, 2078–2079.

Introduced in R2010b


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