[ADAM-914] Create a GenomicRegionPartitioner given a partition count.

adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala

@@ -102,11 +102,18 @@ case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Lon
 
 object GenomicPositionPartitioner {
 
+ /**
+ * Creates a GenomicRegionPartitioner with a specific number of partitions.
+ *
+ * @param numParts The number of partitions to have in the new partitioner.
+ * @param seqDict A sequence dictionary describing the known genomic contigs.
+ * @return Returns a partitioner that divides the known genome into a set number of partitions.
+ */
  def apply(numParts: Int, seqDict: SequenceDictionary): GenomicPositionPartitioner =
  GenomicPositionPartitioner(numParts, extractLengthMap(seqDict))
 
- def extractLengthMap(seqDict: SequenceDictionary): Map[String, Long] =
- Map(seqDict.records.toSeq.map(rec => (rec.name, rec.length)): _*)
+ private[rdd] def extractLengthMap(seqDict: SequenceDictionary): Map[String, Long] =
+ seqDict.records.toSeq.map(rec => (rec.name, rec.length)).toMap
 }
 
 case class GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true) extends Partitioner with Logging {
@@ -140,6 +147,26 @@ case class GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String,
 }
 
 object GenomicRegionPartitioner {
+
+ /**
+ * Creates a GenomicRegionPartitioner where partitions cover a specific range of the genome.
+ *
+ * @param partitionSize The number of bases in the reference genome that each partition should cover.
+ * @param seqDict A sequence dictionary describing the known genomic contigs.
+ * @return Returns a partitioner that divides the known genome into partitions of fixed size.
+ */
  def apply(partitionSize: Long, seqDict: SequenceDictionary): GenomicRegionPartitioner =
  GenomicRegionPartitioner(partitionSize, GenomicPositionPartitioner.extractLengthMap(seqDict))
+
+ /**
+ * Creates a GenomicRegionPartitioner with a specific number of partitions.
+ *
+ * @param numParts The number of partitions to have in the new partitioner.
+ * @param seqDict A sequence dictionary describing the known genomic contigs.
+ * @return Returns a partitioner that divides the known genome into a set number of partitions.
+ */
+ def apply(numParts: Int, seqDict: SequenceDictionary): GenomicRegionPartitioner = {
+ val lengths = GenomicPositionPartitioner.extractLengthMap(seqDict)
+ GenomicRegionPartitioner(lengths.values.sum / numParts, lengths)
+ }
 }