CIGAR

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

Collaboration diagram for CIGAR:

Classes
class	seqan3::cigar
	The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter. More...
struct	seqan3::cigar_printer< cigar >
	The printer used for formatted output of the cigar alphabets. More...

Detailed Description

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

See also

Alphabet

Introduction

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::operation 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::operation 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::operation alphabet.

OP	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 seqan3::sam_record::sequence)
H	Hard clipping (clipped sequences NOT present in seqan3::sam_record::sequence)
P	Padding (silent deletion from padded reference)
=	Sequence match
X	Sequence mismatch