SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.

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...
 

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