From 81defaad834f5a8726998f3df625d472e79950f0 Mon Sep 17 00:00:00 2001
From: tomasznazarewicz <t.nazarewicz94@gmail.com>
Date: Sat, 14 Nov 2020 18:11:17 +0100
Subject: [PATCH] working chromo-sweep

---
 generated/README.md                           |  20 +++
 generated/denser-labels/results/part-00000    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00001    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00002    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00003    | 127 ++++++++++++++++
 generated/denser-labels/results/part-00004    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00005    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00006    | 126 ++++++++++++++++
 generated/denser-labels/results/part-00007    | 127 ++++++++++++++++
 generated/denser-queries/results/part-00000   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00001   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00002   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00003   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00004   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00005   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00006   | 135 ++++++++++++++++++
 generated/denser-queries/results/part-00007   | 135 ++++++++++++++++++
 .../generation/TestDataGenerator.scala        |  44 ++++++
 .../methods/chromosweep/ChromoSweep.scala     |  58 ++++++++
 .../methods/chromosweep/ChromoSweepJoin.scala |  51 +++++++
 .../chromosweep/ChromoSweepJoinImpl.scala     |  95 ++++++++++++
 .../chromosweep/ChromoSweepJoinStrategy.scala |  15 ++
 .../methods/chromosweep/RangeTreeNode.scala   |  32 +++++
 .../methods/chromosweep/SortedInterval.scala  |  11 ++
 .../tests/rangejoins/ChromoSweepTest.scala    |  81 +++++++++++
 25 files changed, 2497 insertions(+)
 create mode 100644 generated/README.md
 create mode 100644 generated/denser-labels/results/part-00000
 create mode 100644 generated/denser-labels/results/part-00001
 create mode 100644 generated/denser-labels/results/part-00002
 create mode 100644 generated/denser-labels/results/part-00003
 create mode 100644 generated/denser-labels/results/part-00004
 create mode 100644 generated/denser-labels/results/part-00005
 create mode 100644 generated/denser-labels/results/part-00006
 create mode 100644 generated/denser-labels/results/part-00007
 create mode 100644 generated/denser-queries/results/part-00000
 create mode 100644 generated/denser-queries/results/part-00001
 create mode 100644 generated/denser-queries/results/part-00002
 create mode 100644 generated/denser-queries/results/part-00003
 create mode 100644 generated/denser-queries/results/part-00004
 create mode 100644 generated/denser-queries/results/part-00005
 create mode 100644 generated/denser-queries/results/part-00006
 create mode 100644 generated/denser-queries/results/part-00007
 create mode 100644 src/main/scala/org/biodatageeks/rangejoins/generation/TestDataGenerator.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweep.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoin.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinImpl.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinStrategy.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/RangeTreeNode.scala
 create mode 100644 src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/SortedInterval.scala
 create mode 100644 src/test/scala/org/biodatageeks/sequila/tests/rangejoins/ChromoSweepTest.scala

diff --git a/generated/README.md b/generated/README.md
new file mode 100644
index 00000000..79b85307
--- /dev/null
+++ b/generated/README.md
@@ -0,0 +1,20 @@
+# Directory for generated test files.
+Files are generated with org.biodatageeks.rangejoins.generation.TestDataGenerator
+
+## Generation parameters
+Data is generated semi-randomly with following parameters:
+
+- amount - amount of intervals to generate
+- maxOffset - max interval to start generation
+- maxRange - max size of interval
+- maxStep - max space between intervals
+
+## Datasets
+Parameters for generated datasets
+1. Denser Labels (expecting less nulls after join)
+    - queries [1000, 50, 5, 30]
+    - labes [1000, 50, 15, 20]
+
+2. Denser Queries (expecting more nulls after join)
+    - queries [1000, 50, 15, 20]
+    - labels [1000, 50, 5, 30]
\ No newline at end of file
diff --git a/generated/denser-labels/results/part-00000 b/generated/denser-labels/results/part-00000
new file mode 100644
index 00000000..3546f2d4
--- /dev/null
+++ b/generated/denser-labels/results/part-00000
@@ -0,0 +1,126 @@
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diff --git a/generated/denser-labels/results/part-00001 b/generated/denser-labels/results/part-00001
new file mode 100644
index 00000000..b442e47c
--- /dev/null
+++ b/generated/denser-labels/results/part-00001
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diff --git a/generated/denser-labels/results/part-00002 b/generated/denser-labels/results/part-00002
new file mode 100644
index 00000000..8d0e31cc
--- /dev/null
+++ b/generated/denser-labels/results/part-00002
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diff --git a/generated/denser-labels/results/part-00003 b/generated/denser-labels/results/part-00003
new file mode 100644
index 00000000..598116de
--- /dev/null
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diff --git a/generated/denser-labels/results/part-00004 b/generated/denser-labels/results/part-00004
new file mode 100644
index 00000000..52c6e946
--- /dev/null
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diff --git a/generated/denser-labels/results/part-00005 b/generated/denser-labels/results/part-00005
new file mode 100644
index 00000000..5ed074fb
--- /dev/null
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diff --git a/generated/denser-labels/results/part-00006 b/generated/denser-labels/results/part-00006
new file mode 100644
index 00000000..47bf4de6
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diff --git a/generated/denser-labels/results/part-00007 b/generated/denser-labels/results/part-00007
new file mode 100644
index 00000000..b99127e1
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diff --git a/generated/denser-queries/results/part-00000 b/generated/denser-queries/results/part-00000
new file mode 100644
index 00000000..eb90f8fb
--- /dev/null
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diff --git a/generated/denser-queries/results/part-00001 b/generated/denser-queries/results/part-00001
new file mode 100644
index 00000000..57cbce29
--- /dev/null
+++ b/generated/denser-queries/results/part-00001
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diff --git a/generated/denser-queries/results/part-00002 b/generated/denser-queries/results/part-00002
new file mode 100644
index 00000000..dc3e34e9
--- /dev/null
+++ b/generated/denser-queries/results/part-00002
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diff --git a/generated/denser-queries/results/part-00003 b/generated/denser-queries/results/part-00003
new file mode 100644
index 00000000..b18a751d
--- /dev/null
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diff --git a/generated/denser-queries/results/part-00004 b/generated/denser-queries/results/part-00004
new file mode 100644
index 00000000..f17189ed
--- /dev/null
+++ b/generated/denser-queries/results/part-00004
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diff --git a/generated/denser-queries/results/part-00005 b/generated/denser-queries/results/part-00005
new file mode 100644
index 00000000..d1f7efbb
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+++ b/generated/denser-queries/results/part-00005
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diff --git a/generated/denser-queries/results/part-00006 b/generated/denser-queries/results/part-00006
new file mode 100644
index 00000000..4e0432ae
--- /dev/null
+++ b/generated/denser-queries/results/part-00006
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diff --git a/generated/denser-queries/results/part-00007 b/generated/denser-queries/results/part-00007
new file mode 100644
index 00000000..aa50d6d5
--- /dev/null
+++ b/generated/denser-queries/results/part-00007
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diff --git a/src/main/scala/org/biodatageeks/rangejoins/generation/TestDataGenerator.scala b/src/main/scala/org/biodatageeks/rangejoins/generation/TestDataGenerator.scala
new file mode 100644
index 00000000..0329585b
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/rangejoins/generation/TestDataGenerator.scala
@@ -0,0 +1,44 @@
+package org.biodatageeks.rangejoins.generation
+
+import org.apache.spark.sql.SparkSession
+
+import scala.collection.mutable
+import scala.util.Random
+
+object TestDataGenerator {
+  def main(args: Array[String]): Unit = {
+    val queryPath = "generated/query"
+    val labelPath = "generated/label"
+    val spark = SparkSession.builder().master("local[*]").appName("generator").getOrCreate()
+    val query = generateRangesList(1000, 50, 5,30).map(rr => QueryRecord(rr.start, rr.end, s"q${rr.index}"))
+    val label = generateRangesList(1000, 50, 15,20).map(rr => LabelRecord(rr.start, rr.end, s"l${rr.index}"))
+    import spark.sqlContext.implicits._
+    spark.sparkContext.parallelize(query).toDF.write.csv(queryPath)
+    spark.sparkContext.parallelize(label).toDF.write.csv(labelPath)
+    // brute force join
+    val joined = query.map(q=> (q,label.filter(l => q.end >= l.start && q.start <= l.end)))
+      .map(e=> if(e._2.isEmpty) (e._1, Seq(LabelRecord(0,0,null)).toList) else e)
+      .flatMap(e=> e._2.map(l=>(e._1, l)))
+      .map(e=>s"${e._1.start},${e._1.end},${e._1.value},${e._2.start},${e._2.end},${e._2.value}")
+    spark.sparkContext.parallelize(joined).saveAsTextFile("generated/result")
+  }
+
+  def generateRangesList(amount: Int, maxOffset: Int, maxRange: Int, maxStep: Int): Seq[RangeRecord] = {
+    val r = new Random()
+    var offset = r.nextInt(maxOffset)
+    var list = new mutable.MutableList[RangeRecord]()
+    for (i <- Range(0, amount)) {
+      val size = r.nextInt(maxRange - 1) + 1
+      val step = r.nextInt(maxStep - 1) + 1
+      list += RangeRecord(offset, offset+size, i)
+      offset = offset + size + step
+    }
+    list
+  }
+}
+
+case class RangeRecord(start: Int, end: Int, index: Int)
+
+case class QueryRecord(start: Int, end: Int, value: String)
+
+case class LabelRecord(start: Int, end: Int, value: String)
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweep.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweep.scala
new file mode 100644
index 00000000..c4b79f8c
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweep.scala
@@ -0,0 +1,58 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+import org.apache.spark.sql.catalyst.InternalRow
+
+import scala.collection.mutable
+
+
+/**
+  * Contains all methods and fields necessary to perform chromo-sweep.
+  */
+class ChromoSweep extends Serializable {
+
+  var lastQuery: Option[(SortedInterval[Int], InternalRow)] = None
+  var lastLabel: Option[(SortedInterval[Int], InternalRow)] = None
+  val mutList: mutable.MutableList[JoinedRow] = mutable.MutableList[JoinedRow]()
+  // push value to result
+  def push = mutList += JoinedRow(lastQuery, lastLabel)
+  // update value of last label
+  def updateLabel(i: (Boolean, SortedInterval[Int], InternalRow)):Unit = lastLabel = Some((i._2, i._3))
+  // update value of last query
+  def updateQuery(i: (Boolean, SortedInterval[Int], InternalRow)):Unit = lastQuery = Some((i._2, i._3))
+  // clears value of label
+  def flushLabel:Unit = lastLabel = None
+  // clears value of query
+  def flushQuery:Unit = lastQuery = None
+
+  /**
+    * Based on the state of the object and given element decides what action should be performed.
+    * @param i
+    */
+  def next(i: (Boolean, SortedInterval[Int], InternalRow)):Unit = {
+    (
+      i._1, //if record is query (true) or a label (false)
+      lastQuery.isDefined, // is there a query that we need to flush or push?
+      lastLabel.isDefined, // is there a label that we need to flush or push?
+      lastQuery.isDefined && i._2.start > lastQuery.get._1.end, // if start of current record is after end of last query
+      lastLabel.isDefined && i._2.start > lastLabel.get._1.end) // if start of current record is after end of last label
+    match {
+      case (false, false, _, _, _) => updateLabel(i)
+      case (false, true, false, true, _) => push; flushQuery; updateLabel(i)
+      case (false, true, false, false, _) => updateLabel(i)
+      case (false, _, true, _, false) => throw new IllegalStateException("Overlapping of two labels")
+      case (false, true, true, false, true) => push; updateLabel(i)
+      case (false, true, true, true, true) => push; flushQuery; updateLabel(i)
+      case (true, false, false, _, _) => updateQuery(i)
+      case (true, false, true, _, true) => flushLabel; updateQuery(i)
+      case (true, false, true, _, false) => updateQuery(i)
+      case (true, true, _, false, _) => throw new IllegalStateException("Overlapping of two queries")
+      case (true, true, false, _, _) => push; updateQuery(i)
+      case (true, true, true, true, false) => push; updateQuery(i)
+      case (true, true, true, _, true) => push; flushLabel; updateQuery(i)
+      case (a, b, c, d, e) => throw new IllegalStateException(s"unknown case: $a $b $c $d $e")
+    }
+  }
+}
+
+
+case class JoinedRow(q: Option[(SortedInterval[Int], InternalRow)], l: Option[(SortedInterval[Int], InternalRow)])
\ No newline at end of file
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoin.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoin.scala
new file mode 100644
index 00000000..bfbb7e4e
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoin.scala
@@ -0,0 +1,51 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+import org.apache.spark.rdd.RDD
+import org.apache.spark.sql.SparkSession
+import org.apache.spark.sql.catalyst.InternalRow
+import org.apache.spark.sql.catalyst.expressions.codegen.GenerateUnsafeRowJoiner
+import org.apache.spark.sql.catalyst.expressions.{Expression, InterpretedProjection, UnsafeRow}
+import org.apache.spark.sql.catalyst.plans.logical.LogicalPlan
+import org.apache.spark.sql.execution.{BinaryExecNode, SparkPlan}
+// logic copied from IntervalTreeJoinOptim
+case class ChromoSweepJoin(left: SparkPlan,
+                           right: SparkPlan,
+                           condition: Seq[Expression],
+                           context: SparkSession, leftLogicalPlan: LogicalPlan, righLogicalPlan: LogicalPlan) extends BinaryExecNode {
+
+  def output = left.output ++ right.output
+
+  lazy val (buildPlan, streamedPlan) = (left, right)
+
+  lazy val (buildKeys, streamedKeys) = (List(condition(0), condition(1)),
+    List(condition(2), condition(3)))
+
+  @transient lazy val buildKeyGenerator = new InterpretedProjection(buildKeys, buildPlan.output)
+  @transient lazy val streamKeyGenerator = new InterpretedProjection(streamedKeys,
+    streamedPlan.output)
+
+  protected override def doExecute(): RDD[InternalRow] = {
+    val v1 = left.execute()
+    val v1kv = v1.map(x => {
+      val v1Key = buildKeyGenerator(x)
+
+      (new SortedInterval[Int](v1Key.getInt(0), v1Key.getInt(1)),
+        x.copy())
+    })
+    val v2 = right.execute()
+    val v2kv = v2.map(x => {
+      val v2Key = streamKeyGenerator(x)
+      (new SortedInterval[Int](v2Key.getInt(0), v2Key.getInt(1)),
+        x.copy())
+    })
+
+    val v3 = ChromoSweepJoinImpl.overlapJoin(context.sparkContext, v1kv, v2kv)
+    v3.map {
+      case (l: InternalRow, r: InternalRow) => {
+        val joiner = GenerateUnsafeRowJoiner.create(left.schema, right.schema);
+        joiner.join(l.asInstanceOf[UnsafeRow], r.asInstanceOf[UnsafeRow]).asInstanceOf[InternalRow] //resultProj(joinedRow(l, r)) joiner.joiner
+      }
+    }
+  }
+}
+
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinImpl.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinImpl.scala
new file mode 100644
index 00000000..e318b2f0
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinImpl.scala
@@ -0,0 +1,95 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+import org.apache.spark.rdd.{RDD, ShuffledRDD}
+import org.apache.spark.sql.catalyst.InternalRow
+import org.apache.spark.{RangePartitioner, SparkContext}
+
+object ChromoSweepJoinImpl extends Serializable {
+
+
+  type K = SortedInterval[Int]
+  type V = (Boolean, SortedInterval[Int], InternalRow)
+
+  /**
+   * Multi-joins together two RDDs that contain objects that map to reference regions.
+   * The object from both sets will be joined using distributed version of the chromo-sweep algorithm.
+   * The basic assumption is that all the intervals from specific range will be on one partition.
+   * Process has following steps:
+   * - create RangePartitioner from RDD1
+   * - partition RDD1 using partitioner
+   * - create range tree where the leaves are pairs of lowest starting and highest ending value of the intervals in a partition
+   * - based on that, map RDD2 to split intervals that belong to multiple partitions and remove the ones that belong to none
+   * - partition mapped RDD2 using previously created partitioner
+   * - union both RDDs
+   * - sort based on start value of the interval
+   * - execute chromo-sweep on each partition.
+   *
+   * @param sc
+   * @param rdd1 - first rdd to join (queries)
+   * @param rdd2 - second rdd to join (labels)
+   * @return
+   */
+  def overlapJoin(sc: SparkContext, rdd1: RDD[(SortedInterval[Int], InternalRow)], rdd2: RDD[(SortedInterval[Int], InternalRow)])
+  : RDD[(InternalRow, InternalRow)] = {
+    // partiton first RDD and based on get range of each partition
+    val tRDD1 = rdd1.map(e => (e._1, (true, e._1, e._2)))
+    val part = new RangePartitioner(tRDD1.getNumPartitions, tRDD1)
+    val rangeTree = getRangeTree(new ShuffledRDD[K, V, V](tRDD1, part))
+    // based on the ranges partition second RDD, split intervals that belong to more than one
+    // remove the ones that belong to none
+    val tRDD2 = rdd2.flatMap(e => rangeTree.getPartitions(e._1).map((_, (false, e._1, e._2))))
+    val uRDD = new ShuffledRDD[K, V, V](tRDD1.union(tRDD2), part)
+    // in each partition do chromosweep
+    uRDD.mapPartitions { p =>
+      val row = p.map(_._2).toList.sortBy(_._2.start).iterator
+      val temp = new ChromoSweep()
+      var i: V = null
+      while (row.hasNext) {
+        i = row.next()
+        temp.next(i)
+      }
+      if (i._1 || temp.lastQuery.isDefined) {
+        temp.push
+      }
+      // in case if there is no label for query we need to replace None with dummy internal row.
+      val dummyInternalRow = createDummyInternalRow(temp)
+      temp.mutList
+        .map(e => (e.q.get._2, e.l.getOrElse((SortedInterval[Int](0, 0), dummyInternalRow))._2)).iterator
+    }
+  }
+
+  private def createDummyInternalRow(temp: ChromoSweep) = {
+    val ir = temp.mutList.head.q.get._2.copy()
+    Range(0, ir.numFields).foreach(i => ir.setNullAt(i))
+    ir
+  }
+
+  private def getRangeTree(rdd: RDD[(K, V)]) = {
+    val arr = getPartitionRanges(rdd)
+    new RangeTreeNode(arr)
+  }
+
+  /**
+   * Calculates sum of all intervals for each partition
+   * e.g. for parititon with intervals [1,3], [5,8], [11, 15] the result is [1,15]
+   *
+   * @param rdd
+   * @return Array of sorted intervals for each parittion
+   */
+  private def getPartitionRanges(rdd: RDD[(K, V)]) = {
+    rdd.mapPartitions(
+      {
+        p =>
+          val temp = p.next()._1
+          var max = temp.end
+          var min = temp.start
+          for (i <- p) {
+            if (min > i._1.start) min = i._1.start
+            if (max < i._1.end) max = i._1.end
+          }
+          (SortedInterval[Int](min, max) :: Nil).iterator
+      }, true)
+      .collect().sortBy(_.start)
+  }
+}
+
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinStrategy.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinStrategy.scala
new file mode 100644
index 00000000..1b18bdfd
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/ChromoSweepJoinStrategy.scala
@@ -0,0 +1,15 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+import org.apache.spark.sql.catalyst.expressions.PredicateHelper
+import org.apache.spark.sql.catalyst.plans.logical.LogicalPlan
+import org.apache.spark.sql.execution.SparkPlan
+import org.apache.spark.sql.{SparkSession, Strategy}
+import org.biodatageeks.sequila.rangejoins.common.ExtractRangeJoinKeys
+
+class ChromoSweepJoinStrategy(spark: SparkSession) extends Strategy with Serializable with  PredicateHelper {
+  def apply(plan: LogicalPlan): Seq[SparkPlan] = plan match {
+    case ExtractRangeJoinKeys(joinType, rangeJoinKeys, left, right) =>
+     ChromoSweepJoin(planLater(left), planLater(right), rangeJoinKeys, spark,left,right) :: Nil
+    case _ => Nil
+  }
+}
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/RangeTreeNode.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/RangeTreeNode.scala
new file mode 100644
index 00000000..40ea2b72
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/RangeTreeNode.scala
@@ -0,0 +1,32 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+case class RangeTreeNode(range: SortedInterval[Int], left: Option[RangeTreeNode], right: Option[RangeTreeNode]) {
+
+  /**
+   * Creates tree structure based on given list of intervals. Each parent note is sum of childes intervals.
+   *
+   * @param si - list of intervals
+   */
+  def this(si: Array[SortedInterval[Int]]) = this(
+    SortedInterval[Int](si.head.start, si.last.end),
+    if (si.length > 1) Some(new RangeTreeNode(si.slice(0, si.length / 2))) else None,
+    if (si.length > 1) Some(new RangeTreeNode(si.slice(si.length / 2, si.length))) else None)
+
+  /**
+   * Retruns list of partitions to which given interval should belong.
+   * One interval can belong to zero or more ranges.
+   * @param si - interval
+   * @return
+   */
+  def getPartitions(si: SortedInterval[Int]): Seq[SortedInterval[Int]] = {
+    if (si.intersects(this.range)) {
+      if (this.left.isEmpty)
+        range :: Nil
+      else
+        this.left.get.getPartitions(si) ++ this.right.get.getPartitions(si)
+    }
+    else {
+      Nil
+    }
+  }
+}
diff --git a/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/SortedInterval.scala b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/SortedInterval.scala
new file mode 100644
index 00000000..233cc4c3
--- /dev/null
+++ b/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/chromosweep/SortedInterval.scala
@@ -0,0 +1,11 @@
+package org.biodatageeks.sequila.rangejoins.methods.chromosweep
+
+case class SortedInterval[T](start: T, end: T)(implicit ev$1: T => Int) extends Ordered[SortedInterval[T]]{
+  def haveStarted(point: T): Boolean = {
+    start < point
+  }
+  def intersects(other: SortedInterval[T]) = {
+    start <= other.end && end >= other.start
+  }
+  override def compare(that: SortedInterval[T]): Int =  if(start < that.start) -1 else if(start > that.start) 1 else 0
+}
diff --git a/src/test/scala/org/biodatageeks/sequila/tests/rangejoins/ChromoSweepTest.scala b/src/test/scala/org/biodatageeks/sequila/tests/rangejoins/ChromoSweepTest.scala
new file mode 100644
index 00000000..1a00f269
--- /dev/null
+++ b/src/test/scala/org/biodatageeks/sequila/tests/rangejoins/ChromoSweepTest.scala
@@ -0,0 +1,81 @@
+package org.biodatageeks.sequila.tests.rangejoins
+
+import com.holdenkarau.spark.testing.DataFrameSuiteBase
+import org.apache.spark.sql.Row
+import org.apache.spark.sql.types.{IntegerType, StringType, StructField, StructType}
+import org.biodatageeks.sequila.rangejoins.methods.chromosweep.ChromoSweepJoinStrategy
+import org.scalatest.{BeforeAndAfter, FunSuite}
+
+class ChromoSweepTest
+  extends FunSuite
+    with DataFrameSuiteBase
+    with BeforeAndAfter {
+  val oneFieldSchema = StructType(
+    Seq(StructField("start", IntegerType)))
+  val twoFieldSchema = StructType(
+    Seq(StructField("start", IntegerType),
+      StructField("end", IntegerType)))
+
+  val resultSchema = StructType(Seq(
+    StructField("start1", IntegerType),
+    StructField("end1", IntegerType),
+    StructField("rval1", StringType),
+    StructField("start2", IntegerType),
+    StructField("end2", IntegerType),
+    StructField("rval2", StringType)))
+
+  before {
+    spark.experimental.extraStrategies = new ChromoSweepJoinStrategy(spark) :: Nil
+
+    val rdd1 = sc
+      .parallelize(Seq((100, 190), (200, 290), (400, 600), (10000, 20000), (22100, 22100)))
+      .map(i => Row(i._1.toInt, i._2.toInt))
+    val rdd2 = sc
+      .parallelize(Seq((150, 180), (190, 300), (310, 500), (510, 700), (22000, 22300), (15000, 15000)))
+      .map(i => Row(i._1.toInt, i._2.toInt))
+
+    val ds1 = sqlContext.createDataFrame(rdd1, twoFieldSchema)
+    ds1.createOrReplaceTempView("s1")
+    val ds2 = sqlContext.createDataFrame(rdd2, twoFieldSchema)
+    ds2.createOrReplaceTempView("s2")
+  }
+
+  test("simple functionality test") {
+    val query = "select s1.start from s1 join s2 on (s1.end >= s2.start and s1.start <= s2.end)"
+    assertDataFrameEquals(
+      sqlContext
+        .createDataFrame(
+          sc.parallelize(Row(100) :: Row(100) :: Row(200) :: Row(400) :: Row(400) :: Row(10000) :: Row(22100) :: Nil),
+          oneFieldSchema)
+        .orderBy("start"),
+      sqlContext.sql(query).orderBy("s1.start")
+    )
+  }
+
+  // tests on bigger datasets
+
+  test("test denser queries") {
+    testGeneratedData("generated/denser-queries/queries/", "generated/denser-queries/labels/", "generated/denser-queries/results")
+  }
+
+  test("test denser labels") {
+    testGeneratedData("generated/denser-labels/queries/", "generated/denser-labels/labels/", "generated/denser-labels/results")
+  }
+
+
+  private def testGeneratedData(queryPath: String, labelPath: String, resultPath: String) = {
+    import spark.implicits._
+    // workaround to avoid serialization error for CSVParser
+    val ds3 = spark.sparkContext.textFile(queryPath).map(_.split(",")).map(e => (e(0).toInt, e(1).toInt, e(2))).toDF("start1", "end1", "val1")
+    ds3.createOrReplaceTempView("dq1")
+    val ds4 = spark.sparkContext.textFile(labelPath).map(_.split(",")).map(e => (e(0).toInt, e(1).toInt, e(2))).toDF("start2", "end2", "val2")
+    ds4.createOrReplaceTempView("dq2")
+    val expected = spark.read.schema(resultSchema).csv(resultPath)
+    val sqlQuery1 = "select * from dq1 join dq2 on (end1 >= start2 and start1 <= end2)"
+    val result = sqlContext.sql(sqlQuery1)
+    val joined = result.join(expected, Seq("start1", "end1", "start2", "end2"))
+    assertTrue(joined.where("(dq2.val2 == null and rval2 != null) or (dq2.val2 != null and rval2 == null)").count() == 0)
+    assertTrue(joined.where("(dq2.val2 != null and rval2 != null) and dq2.val2 != rval2").count() == 0)
+  }
+
+}
\ No newline at end of file