au.csiro.variantspark.algo.metrics.Metrics.scala Maven / Gradle / Ivy

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Genomic variants interpretation toolkit

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package au.csiro.variantspark.algo.metrics

import au.csiro.variantspark.algo.AggregablePairwiseOperation
import au.csiro.variantspark.algo.PairwiseOperation

object EuclideanPairwiseMetric extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = (b1 - b2).toLong * (b1 - b2).toLong
  override def finalOp(result: Array[Long]): Array[Double] =
    result.map(l => Math.sqrt(l.toDouble))
}

object ManhattanPairwiseMetric extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = Math.abs(b1 - b2).toLong
}

@deprecated
object BitwiseAndPairwiseRevMetric extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = (b1 & b2).toLong
}

@deprecated
object MultiPairwiseRevMetric extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = b1.toLong * b2.toLong
}

object SharedAltAlleleCount extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = Math.min(b1.toLong, b2.toLong)
}

object AtLeastOneSharedAltAlleleCount extends AggregablePairwiseOperation {
  def unitOp(b1: Byte, b2: Byte): Long = {
    val noOfSharedAlt = Math.min(b1.toLong, b2.toLong)
    if (noOfSharedAlt > 0) 1 else 0
  }
}