ReferenceRegion
Related Docs:
class ReferenceRegion
| package models
Creates a reference region that covers the entirety of a contig.
Creates a reference region that covers the entirety of a contig.
The name of the reference contig to cover.
The strand of the genome that this region exists on.
Returns a reference region that covers the entirety of a contig.
Builds a reference region for a coverage site.
Builds a reference region for a coverage site.
Coverage to extract ReferenceRegion from
Extracted ReferenceRegion
Generates a reference region from assembly data.
Generates a reference region from assembly data. Returns None if the assembly does not have an ID or a start position.
Assembly fragment from which to generate data.
Region corresponding to inclusive region of contig fragment.
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.
The position to convert
A 1-wide region at the same location as pos
Builds a reference region for a variant site.
Builds a reference region for a variant site.
Variant to extract region from.
The site where this variant covers.
Builds a reference region for a called genotype.
Builds a reference region for a called genotype.
Called genotype to extract region from.
The site where this genotype lives.
Creates a predicate that filters records overlapping one or more regions.
Creates a predicate that filters records overlapping one or more regions.
The regions to filter on.
Returns a predicate that can be pushed into Parquet files that keeps all records that overlap one or more region.
Creates a reference region that starts at the beginning of a contig.
Creates a reference region that starts at the beginning of a contig.
The name of the reference contig that this region is on.
The end position for this region.
The strand of the genome that this region exists on.
Returns a reference region that goes from the start of a contig to a user provided end point.
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
The string describing the loci to create reference regions for.
Returns an iterable collection of reference regions.
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.
Read to create region from.
Region corresponding to inclusive region of read alignment, if read is mapped.
Builds a reference region for a feature with strand set.
Builds a reference region for a feature with strand set.
Feature to extract ReferenceRegion from.
Extracted ReferenceRegion
IllegalArgumentException Throws an exception if the strand is null
in the provided feature.
unstranded
Builds a reference region for an aligned read with strand set.
Builds a reference region for an aligned read with strand set.
The read to extract the reference region from.
Returns the reference region covered by this read's alignment.
IllegalArgumentException If this read is not aligned, alignment
data is null, or strand is not set.
unstranded
Creates a reference region that has an open end point.
Creates a reference region that has an open end point.
The name of the reference contig that this region is on.
The start position for this region.
The strand of the genome that this region exists on.
Returns a reference region that goes from a user provided starting point to the end of a contig.
Builds a reference region for a feature without strand information.
Builds a reference region for a feature without strand information.
Feature to extract ReferenceRegion from.
Extracted ReferenceRegion
stranded
Builds a reference region with independent strand for an aligned read.
Builds a reference region with independent strand for an aligned read.
The read to extract the reference region from.
Returns the reference region covered by this read's alignment.
IllegalArgumentException If this read is not aligned or alignment
data is null.
stranded
A companion object for creating and ordering ReferenceRegions.