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CIGAR
Alphabet

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

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