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.
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).
Generates a reference position from a pileup base.
Generates a reference position from a pileup base. Pileups are mapped by definition, so no option wrapper is required.
A single pileup base.
The reference position of this pileup.
Generates a reference position from a genotype.
Generates a reference position from a genotype.
Genotype from which to generate a reference position.
The reference position of this genotype.
An invariant of genotypes is that they have a defined position, therefore we do not wrap them in an option.
Generates a reference position from a called variant.
Generates a reference position from a called variant.
Called variant from which to generate a reference position.
The reference position of this variant.
An invariant of variants is that they have a defined position, therefore we do not wrap them in an option.
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.
Read from which to generate a reference position.
Reference position wrapped inside of an option. If the read is mapped, the option will be stuffed, else it will be empty (None).
fivePrime
Generates a reference position from the five prime end of a read.
Generates a reference position from the five prime end of a read. This will be different from the start mapping position of a read if this read is a reverse strand read.
Read from which to generate a reference position.
Reference position wrapped inside of an option. If the read is mapped, the option will be stuffed, else it will be empty (None).
apply(record: Read)
Checks to see if a read is mapped with a valid position.
Checks to see if a read is mapped with a valid position.
Read to check for mapping.
True if read is mapped and has a valid position, else false.