Crate biodiff_align 

This module contains bindings for the alignment algorithms used in biodiff. The main interface are the methods of the AlignAlgorithm struct.

If handling of selections and semiglobal alignment is needed, the AlignInfo struct should be used.

Before running the alignment, the parameters should be checked with the AlignAlgorithm::check_parameters or AlignInfo::check_parameters methods.

Most methods are meant for a gradual alignment of files, but the AlignAlgorithm::align_whole method is the simplest interface and can be used to align two files as a whole synchronously.

The gradual alignment first sends an AlignedMessage::Initial message with the initial block of bytes, then sends AlignedMessage::Append and AlignedMessage::Prepend messages with the rest of the bytes.

Re-exports

pub use self::rustbio::Banded;

Modules

rustbio

wfa2

Structs

AlignAlgorithm

Contains parameters to run the alignment algorithm with

AlignElement

Representation of the alignment that saves the original addresses of the bytes. This has some space overhead, but alignment is slow enough for that not to matter in most cases.

AlignInfo

A bundle of two alignment algorithms, one for global alignment and one for semiglobal alignment.

Enums

AlgorithmKind

AlignBackend

The backend used for alignment

AlignMode

An align mode, can be either Local for local alignment, global for global alignment, or Blockwise with a given block size. The blockwise mode starts from a given position and aligns only using blocksize bytes from each sequence in one direction, which makes it works fast and local, but it doesn’t see bigger gaps and everything after big gaps tends to be unaligned.

AlignedMessage

CheckStatus

Constants

DEFAULT_BLOCKSIZE