package alignment
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Type Members
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case class
Alignment
(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
A general class to describe the alignment between two sequences or partial ranges thereof
- query
the query sequence
- target
the target sequence
- queryStart
the 1-based position in the query sequence where the alignment begins
- targetStart
the 1-based position in the target sequence where the alignment begins
- cigar
a Cigar object describing the alignment of the two sequences
- score
the alignment score
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case class
Cigar
(elems: IndexedSeq[CigarElem]) extends Iterable[CigarElem] with Product with Serializable
Object representation of a Cigar string representing an alignment between two sequences.
Object representation of a Cigar string representing an alignment between two sequences.
- elems
the ordered sequence of elements in the Cigar
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case class
CigarElem
(operator: CigarOperator, length: Int) extends Product with Serializable
Represents an element in a Cigar.
Represents an element in a Cigar.
- operator
the type of element (e.g. match, insertion, etc.)
- length
the length of the element in bases (must be greater than 0).
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class
LinearMatrix
[A] extends Matrix[A]
Implements a matrix using a single linear array.
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trait
Matrix
[A] extends AnyRef
Defines methods applicable to a 2D matrix.
Defines methods applicable to a 2D matrix. Matrix cells are accessed with a pair of coordiantes, the first of which is the row offset starting at 0, and the second of which is the column offset, starting at 0.
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class
NeedlemanWunschAligner
extends AnyRef
Implementation of the Needleman-Wunsch algorithm for global alignment of two sequences with support for an affine gap penalty.
Value Members
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object
Alignment
extends Serializable
Companion object for Alignment.
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object
Cigar
extends Serializable
Companion object for Cigar that offers alternative constructors.
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object
Matrix
Factory method(s) for Matrices.
- object NeedlemanWunschAligner