UCSC binning scheme ported to Scala (http://genomewiki.ucsc.edu/index.php/Bin_indexing_system)

bin_index_ucsc.scala

import scala.collection.mutable.ArrayBuffer

def binFromRange(start: Int, end: Int): ArrayBuffer[Int] ={

  val bin_offsets = Array(512+64+8+1,64+8+1,8+1,0)
  val binFirstShift = 17
  val binNextShift = 3


  var startBin = start >> binFirstShift
  var endBin = (end -1) >> binFirstShift


  var binArray = ArrayBuffer[Int]()

  for(i<-bin_offsets){
    val bin = i + startBin
    binArray += bin
    startBin >>= binNextShift
    endBin >>= binNextShift
  } 

  return binArray

  
}