Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
aligned sequences represented in
cell array of aligned strings or a character array, into
a cell array of corresponding CIGAR strings, using the reference sequence
Ref, a string. It also returns
a vector of integers indicating the start position of each aligned
sequence with respect to the ungapped reference sequence.
Cell array of aligned sequence strings 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.
String specifying an aligned reference sequence. The length
Cell array of CIGAR strings corresponding to each aligned sequence
Vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.
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 = '3M1D4M' '4M1D3M' '4M1D1M' start = 1 1 3
 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.