Expand description
Types for representing pairwise sequence alignments
Structs§
- We consider alignment between two sequences x and y. x is the query or read sequence and y is the reference or template sequence. An alignment, consisting of a score, the start and end position of the alignment on sequence x and sequence y, the lengths of sequences x and y, and the alignment edit operations. The start position and end position of the alignment does not include the clipped regions. The length of clipped regions are already encapsulated in the Alignment Operation.
Enums§
- The modes of alignment supported by the aligner include standard modes such as Global, Semi-Global and Local alignment. In addition to this, user can also invoke the custom mode. In the custom mode, users can explicitly specify the clipping penalties for prefix and suffix of strings ‘x’ and ‘y’ independently. Under the hood the standard modes are implemented as special cases of the custom mode with the clipping penalties appropriately set.
- Alignment operations supported are match, substitution, insertion, deletion and clipping. Clipping is a special boundary condition where you are allowed to clip off the beginning/end of the sequence for a fixed clip penalty. The clip penalty could be different for the two sequences x and y, and the clipping operations on both are distinguishable (Xclip and Yclip). The usize value associated with the clipping operations are the lengths clipped. In case of standard modes like Global, Semi-Global and Local alignment, the clip operations are filtered out