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.
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
Builds a reference region for a feature.
Builds a reference region for a feature.
Feature 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 an aligned read.
Builds a reference region for an aligned read.
The read to extract the reference region from.
Returns the reference region covered by this read's alignment.
If this read is not aligned or alignment data is null.
Builds a reference region from a variant annotation.
Builds a reference region from a variant annotation.
VariantAnnotation to extract region from.
The site where the variant for the specified variant annotation covers.
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 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.
Returns a reference region that goes from the start of a contig to a user provided end point.
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.
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.
Returns a reference region that goes from a user provided starting point to the end of a contig.
A companion object for creating and ordering ReferenceRegions.