SeqAn3  3.0.2
The Modern C++ library for sequence analysis.

Provides (semi-)alphabets for representing elements in CIGAR strings. More...

+ Collaboration diagram for CIGAR:


class  seqan3::cigar
 The cigar semialphabet pairs a counter with a seqan3::cigar_op letter. More...
class  seqan3::cigar_op
 The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=. More...

Detailed Description

Provides (semi-)alphabets for representing elements in CIGAR strings.


CIGAR strings are combinations of count values and CIGAR operations, representing an alignment as a sequence of edit operations. This submodule has two different alphabets. One is the seqan3::cigar_op alphabet, which is a base seqan3::alphabet implementation. This contains all valid symbols contained in CIGAR strings. The other alphabet is the seqan3::cigar alphabet, which is an alphabet tuple. It combines the seqan3::cigar_op alphabet with a count value, such that one can represent an entire CIGAR string with a std::vector of seqan3::cigar values.

The following table outlines the valid characters in the seqan3::cigar_op alphabet.

Letter Description
M Alignment match (can be a sequence match or mismatch, used only in basic CIGAR representations)
I Insertion to the reference
D Deletion from the reference
N Skipped region from the reference
S Soft clipping (clipped sequences present in SEQ)
H Hard clipping (clipped sequences NOT present in SEQ)
P Padding (silent deletion from padded reference)
= Sequence match
X Sequence mismatch