Crate pa_types 

Common types for alignments:

Sequence types:

• Base : u8,
• Sequence : Vec<Base>,
• Seq : &[Base].

Affine cost models:

• CostModel,
• ScoreModel.

Alignment path:

• index I : i32,
• position type Pos : (I, I) for (text/ref index, pattern/query index),
• Path : Vec<Pos>.

Cigar strings (see cigar module documentation):

• single character CigarOp : match/sub/ins/del,
• repeated ‘unit’ CigarElem : CigarOp with length,
• cigar string Cigar : Vec<CigarElem>.

Re-exports

pub use cigar::*;

pub use cost::*;

Modules

cigar

Cigar string types.

cost

i32 Cost and Score, affine CostModel and ScoreModel.

Structs

LexPos

A small wrapper around Pos that implements Ord for lexicographic ordering.

Pos

A (text/ref, pattern/query) position in a pairwise alignment.

Traits

Aligner

Generic global pairwise alignment interface.

Functions

seq_to_string

Convert seq to a String.

Type Aliases

Base

A single base

I

A 0-based index into a sequence.

Path

The path corresponding to an alignment of two sequences.

Seq

A slice of bases.

Sequence

A vector of bases.