case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long]) extends Partitioner with Logging with Product with Serializable
GenomicPositionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.
This can be used to organize genomic data for computation that is spatially distributed (e.g. GATK and Queue's "scatter-and-gather" for locus-parallelizable walkers).
- numParts
The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.
- seqLengths
a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.
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GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long])
- numParts
The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.
- seqLengths
a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.
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def
getPartition(key: Any): Int
Computes the partition for a key.
Computes the partition for a key.
- key
A key to compute the partition for.
- returns
The partition that this key belongs to.
- Definition Classes
- GenomicPositionPartitioner → Partitioner
- Exceptions thrown
IllegalArgumentException
if the key is not a ReferencePosition, or (ReferencePosition, _) tuple.
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def
numPartitions: Int
This is the total number of partitions for both mapped and unmapped positions.
This is the total number of partitions for both mapped and unmapped positions. All unmapped positions go into the last partition.
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- GenomicPositionPartitioner → Partitioner
- See also
parts
- val numParts: Int
- val seqLengths: Map[String, Long]
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