object ReferenceRegion extends Serializable
A companion object for creating and ordering ReferenceRegions.
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def
all(referenceName: String, strand: Strand = Strand.INDEPENDENT): ReferenceRegion
Creates a reference region that covers the entirety of a reference sequence.
Creates a reference region that covers the entirety of a reference sequence.
- referenceName
The name of the reference sequence to cover.
- strand
The strand of the genome that this region exists on.
- returns
Returns a reference region that covers the entirety of a reference sequence.
-
def
apply(coverage: Coverage): ReferenceRegion
Builds a reference region for a coverage site.
Builds a reference region for a coverage site.
- coverage
Coverage to extract ReferenceRegion from
- returns
Extracted ReferenceRegion
-
def
apply(slice: Slice): Option[ReferenceRegion]
Generates a reference region from a slice.
Generates a reference region from a slice. Returns None if the slice does not have a name, a start position, or an end position.
- slice
Slice from which to generate data.
- returns
Region corresponding to inclusive region of the specified slice.
-
def
apply(sequence: Sequence): Option[ReferenceRegion]
Generates a reference region from a sequence.
Generates a reference region from a sequence. Returns None if the sequence does not have a name or a length.
- sequence
Sequence from which to generate data.
- returns
Region corresponding to inclusive region of the specified sequence.
-
def
apply(pos: ReferencePosition): ReferenceRegion
Generates a region from a given position -- the region will have a length of 1.
Generates a region from a given position -- the region will have a length of 1.
- pos
The position to convert
- returns
A 1-wide region at the same location as pos
-
def
apply(variant: Variant): ReferenceRegion
Builds a reference region for a variant site.
Builds a reference region for a variant site.
- variant
Variant to extract region from.
- returns
The site where this variant covers.
-
def
apply(genotype: Genotype): ReferenceRegion
Builds a reference region for a called genotype.
Builds a reference region for a called genotype.
- genotype
Called genotype to extract region from.
- returns
The site where this genotype lives.
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def
createPredicate(regions: ReferenceRegion*): FilterPredicate
Creates a predicate that filters records overlapping one or more regions.
Creates a predicate that filters records overlapping one or more regions.
- regions
The regions to filter on.
- returns
Returns a predicate that can be pushed into Parquet files that keeps all records that overlap one or more region.
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def
fromGenomicRange(referenceName: String, start: Long, end: Long): ReferenceRegion
Builds a referenceRegion from genomic coordinates.
Builds a referenceRegion from genomic coordinates.
- referenceName
reference name
- start
start position
- end
end position
- returns
Reference Region for these genomic coordinates
-
def
fromStart(referenceName: String, end: Long, strand: Strand = Strand.INDEPENDENT): ReferenceRegion
Creates a reference region that starts at the beginning of a reference sequence.
Creates a reference region that starts at the beginning of a reference sequence.
- referenceName
The name of the reference sequence that this region is on.
- end
The end position for this region.
- strand
The strand of the genome that this region exists on.
- returns
Returns a reference region that goes from the start of a reference sequence to a user provided end point.
-
def
fromString(loci: String): Iterable[ReferenceRegion]
Parses a set of comma delimited loci from a string.
Parses a set of comma delimited loci from a string.
Acceptable strings include: - ctg:start-end - ctg:pos
- loci
The string describing the loci to create reference regions for.
- returns
Returns an iterable collection of reference regions.
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def
opt(record: Alignment): Option[ReferenceRegion]
Generates a reference region from read data.
Generates a reference region from read data. Returns None if the read is not mapped; else, returns the inclusive region from the start to the end of the read alignment.
- record
Read to create region from.
- returns
Region corresponding to inclusive region of read alignment, if read is mapped.
- implicit def orderingForOptionalPositions: OptionalRegionOrdering.type
- implicit def orderingForPositions: RegionOrdering.type
-
def
stranded(feature: Feature): ReferenceRegion
Builds a reference region for a feature with strand set.
Builds a reference region for a feature with strand set.
- feature
Feature to extract ReferenceRegion from.
- returns
Extracted ReferenceRegion
- Exceptions thrown
IllegalArgumentException
Throws an exception if the strand is null in the provided feature.- See also
unstranded
-
def
stranded(record: Alignment): ReferenceRegion
Builds a reference region for an aligned read with strand set.
Builds a reference region for an aligned read with strand set.
- record
The read to extract the reference region from.
- returns
Returns the reference region covered by this read's alignment.
- Exceptions thrown
IllegalArgumentException
If this read is not aligned, alignment data is null, or strand is not set.- See also
unstranded
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def
toEnd(referenceName: String, start: Long, strand: Strand = Strand.INDEPENDENT): ReferenceRegion
Creates a reference region that has an open end point.
Creates a reference region that has an open end point.
- referenceName
The name of the reference sequence that this region is on.
- start
The start position for this region.
- strand
The strand of the genome that this region exists on.
- returns
Returns a reference region that goes from a user provided starting point to the end of a reference sequence.
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def
unstranded(feature: Feature): ReferenceRegion
Builds a reference region for a feature without strand information.
Builds a reference region for a feature without strand information.
- feature
Feature to extract ReferenceRegion from.
- returns
Extracted ReferenceRegion
- See also
stranded
-
def
unstranded(record: Alignment): ReferenceRegion
Builds a reference region with independent strand for an aligned read.
Builds a reference region with independent strand for an aligned read.
- record
The read to extract the reference region from.
- returns
Returns the reference region covered by this read's alignment.
- Exceptions thrown
IllegalArgumentException
If this read is not aligned or alignment data is null.- See also
stranded
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