object ReferencePosition extends Serializable
Companion object for creating and sorting ReferencePositions.
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val
UNMAPPED: ReferencePosition
The UNMAPPED value is a convenience value, which can be used to indicate a position which is not located anywhere along the reference sequences (see, e.g.
The UNMAPPED value is a convenience value, which can be used to indicate a position which is not located anywhere along the reference sequences (see, e.g. its use in GenomicPositionPartitioner).
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def
apply(referenceName: String, pos: Long, strand: Strand): ReferencePosition
Convenience method for building a ReferencePosition.
Convenience method for building a ReferencePosition.
- referenceName
The name of the reference sequence this locus exists on.
- pos
The position of this locus.
- strand
The strand that this locus is on.
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def
apply(referenceName: String, pos: Long): ReferencePosition
Convenience method for building a ReferencePosition.
Convenience method for building a ReferencePosition.
- referenceName
The name of the reference sequence this locus exists on.
- pos
The position of this locus.
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def
apply(genotype: Genotype): ReferencePosition
Generates a reference position from a genotype.
Generates a reference position from a genotype.
- genotype
Genotype from which to generate a reference position.
- returns
The reference position of this genotype.
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def
apply(variant: Variant): ReferencePosition
Generates a reference position from a called variant.
Generates a reference position from a called variant.
- variant
Called variant from which to generate a reference position.
- returns
The reference position of this variant.
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def
apply(record: Alignment): ReferencePosition
Generates a reference position from a read.
Generates a reference position from a read. This function generates the position from the start mapping position of the read.
- record
Read from which to generate a reference position.
- returns
Reference position of the start position.
- See also
fivePrime
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- implicit def orderingForOptionalPositions: OptionalPositionOrdering.type
- implicit def orderingForPositions: PositionOrdering.type
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