(query: Array[Byte], target: Array[Byte], queryStart: Int, targetStart: Int, cigar: Cigar, score: Int) extends Product with Serializable
A general class to describe the alignment between two sequences or partial ranges thereof
the query sequence
the target sequence
the 1-based position in the query sequence where the alignment begins
the 1-based position in the target sequence where the alignment begins
a Cigar object describing the alignment of the two sequences
the alignment score
(elems: IndexedSeq[CigarElem]) extends Iterable[CigarElem] with Product with Serializable
Object representation of a Cigar string representing an alignment between two sequences.
the ordered sequence of elements in the Cigar
(operator: CigarOperator, length: Int) extends Product with Serializable
Represents an element in a Cigar.
the type of element (e.g. match, insertion, etc.)
the length of the element in bases (must be greater than 0).
[A] extends Matrix[A]
Implements a matrix using a single linear array.
[A] extends AnyRef
Defines methods applicable to a 2D matrix.
Implementation of the Needleman-Wunsch algorithm for global alignment of two sequences with support for an affine gap penalty.