package alignment
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Type Members
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class
Aligner
extends AnyRef
Implementation of an aligner with generic scoring function and affine gap penalty support.
Implementation of an aligner with generic scoring function and affine gap penalty support. Supports multiple alignment Modes for global, semi-global and local alignment.
A scoring function (
scoringFunction) is taken to score pair-wise aligned bases. A default implementation is supplied via the companion Aligner object which uses a fixed match score and mismatch penalty. -
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 coordinates, 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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sealed
trait
Mode
extends EnumEntry
Trait that entries in Mode will extend.
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type
NeedlemanWunschAligner = Aligner
- Annotations
- @deprecated
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Value Members
- object Aligner
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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.
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object
Mode
extends FgBioEnum[Mode]
Enum to represent alignment modes supported by the Aligner.