upgrade plugin, spark-tests, kryo reg

build.sbt

@@ -1,22 +1,21 @@
-
 organization := "org.hammerlab.genomics"
 name := "loci"
-version := "2.0.1"
+r"2.0.1"
 
 addSparkDeps
 
-deps ++= Seq(
+dep(
   args4j,
-  args4s % "1.3.0",
+  args4s       % "1.3.0",
   htsjdk,
-  iterators % "1.3.0",
-  paths % "1.2.0",
+  iterators    % "1.3.0",
+  paths        % "1.2.0",
+  reference    % "1.4.0" + testtest,
   scalautils,
+  spark_util   % "2.0.1",
   string_utils % "1.2.0"
 )
 
-compileAndTestDeps += reference % "1.4.0"
-
 // Shade Guava due to use of RangeSet classes from 16.0.1 that don't exist in Spark/Hadoop's Guava 11.0.2.
 shadedDeps += guava
 

project/build.properties

@@ -1 +1 @@
-sbt.version=0.13.13
+sbt.version=1.0.4

project/plugins.sbt

@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.1.0")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "4.0.0-SNAPSHOT")

src/main/scala/org/hammerlab/genomics/loci/map/Contig.scala

@@ -121,4 +121,8 @@ object Contig {
   }
 
   def lociRange(start: Locus, end: Locus): JRange[Locus] = JRange.closedOpen[Locus](start, end)
+
+  import org.hammerlab.kryo._
+  implicit val serializer = new ContigSerializer[Nothing]
+  implicit val alsoRegister = AlsoRegister[Contig[Nothing]](cls[ContigName])
 }

src/main/scala/org/hammerlab/genomics/loci/map/LociMap.scala

@@ -94,4 +94,9 @@ object LociMap {
         contigs.map(contig => contig.name -> contig).toSeq: _*
       )
     )
+
+  import com.esotericsoftware.kryo
+  import org.hammerlab.kryo._
+  implicit val serializer: kryo.Serializer[LociMap[Nothing]] = new Serializer[Nothing]
+  implicit val alsoRegister = AlsoRegister[LociMap[Nothing]](arr[Contig[Nothing]])
 }

src/main/scala/org/hammerlab/genomics/loci/map/Serializer.scala

@@ -1,22 +1,23 @@
 package org.hammerlab.genomics.loci.map
 
+import com.esotericsoftware.kryo
+import com.esotericsoftware.kryo.Kryo
 import com.esotericsoftware.kryo.io.{ Input, Output }
-import com.esotericsoftware.kryo.{ Kryo, Serializer ⇒ KryoSerializer }
 
 /**
  * We serialize a LociMap simply by writing out all of its Contigs.
  */
-class Serializer[T] extends KryoSerializer[LociMap[T]] {
+class Serializer[T] extends kryo.Serializer[LociMap[T]] {
   def write(kryo: Kryo, output: Output, obj: LociMap[T]) = {
     output.writeLong(obj.contigs.size)
-    obj.contigs.foreach(contig =>
+    obj.contigs.foreach(contig ⇒
       kryo.writeObject(output, contig)
     )
   }
 
   def read(kryo: Kryo, input: Input, klass: Class[LociMap[T]]): LociMap[T] = {
     val count: Long = input.readLong()
-    val contigs = (0L until count).map(i =>
+    val contigs = (0L until count).map(i ⇒
       kryo.readObject(input, classOf[Contig[T]])
     )
     LociMap.fromContigs(contigs)

src/main/scala/org/hammerlab/genomics/loci/set/Contig.scala

@@ -113,4 +113,8 @@ object Contig {
     )
 
   def lociRange(start: Locus, end: Locus): JRange[Locus] = closedOpen[Locus](start, end)
+
+  import org.hammerlab.kryo._
+  implicit val serializer = new ContigSerializer
+  implicit val alsoRegister = AlsoRegister[Contig](cls[ContigName])
 }

src/main/scala/org/hammerlab/genomics/loci/set/ContigSerializer.scala

@@ -6,7 +6,7 @@ import com.google.common.collect.{ TreeRangeSet, Range ⇒ JRange }
 import JRange.closedOpen
 import org.hammerlab.genomics.reference.{ ContigName, Interval, Locus }
 
-// We serialize a LociSet simply by writing out its constituent Contigs.
+/** Serialize a [[LociSet]] simply by writing out its [[Contig]]s. */
 class ContigSerializer extends KryoSerializer[Contig] {
 
   def write(kryo: Kryo, output: Output, obj: Contig) = {

src/main/scala/org/hammerlab/genomics/loci/set/LociSet.scala

@@ -1,5 +1,7 @@
 package org.hammerlab.genomics.loci.set
 
+import com.esotericsoftware.kryo.io.{ Input, Output }
+import com.esotericsoftware.kryo.{ Kryo, Serializer }
 import htsjdk.samtools.util.{ Interval ⇒ HTSJDKInterval }
 import org.hammerlab.genomics.loci.parsing.{ All, LociRange, LociRanges, ParsedLoci }
 import org.hammerlab.genomics.reference.ContigName.Factory
@@ -175,4 +177,20 @@ object LociSet {
             }
       }
     )
+
+  // We just serialize the underlying contigs, which contain their names which are the string keys of LociSet.map.
+  implicit val serializer =
+    new Serializer[LociSet] {
+      def write(kryo: Kryo, output: Output, obj: LociSet) = {
+        kryo.writeObject(output, obj.contigs)
+      }
+
+      def read(kryo: Kryo, input: Input, klass: Class[LociSet]): LociSet = {
+        val contigs = kryo.readObject(input, classOf[Array[Contig]])
+        LociSet.fromContigs(contigs)
+      }
+    }
+
+  import org.hammerlab.kryo._
+  implicit val alsoRegister = AlsoRegister[LociSet](arr[Contig])
 }

src/main/scala/org/hammerlab/genomics/loci/set/Serializer.scala

@@ -3,14 +3,3 @@ package org.hammerlab.genomics.loci.set
 import com.esotericsoftware.kryo.io.{ Input, Output }
 import com.esotericsoftware.kryo.{ Kryo, Serializer ⇒ KryoSerializer }
 
-// We just serialize the underlying contigs, which contain their names which are the string keys of LociSet.map.
-class Serializer extends KryoSerializer[LociSet] {
-  def write(kryo: Kryo, output: Output, obj: LociSet) = {
-    kryo.writeObject(output, obj.contigs)
-  }
-
-  def read(kryo: Kryo, input: Input, klass: Class[LociSet]): LociSet = {
-    val contigs = kryo.readObject(input, classOf[Array[Contig]])
-    LociSet.fromContigs(contigs)
-  }
-}

src/test/scala/org/hammerlab/genomics/loci/map/SerializerSuite.scala

@@ -6,10 +6,14 @@ import org.hammerlab.genomics.reference.{ ContigName, Locus }
 import org.hammerlab.spark.test.suite.{ KryoSparkSuite, SparkSerialization }
 
 class SerializerSuite
-  extends KryoSparkSuite(classOf[Registrar])
+  extends KryoSparkSuite
     with SparkSerialization
     with ClearContigNames {
 
+  register(
+    classOf[LociMap[Nothing]]
+  )
+
   def check(
     ranges: (ContigName, Locus, Locus, String)*
   )(

src/test/scala/org/hammerlab/genomics/loci/set/LociSetSuite.scala

@@ -6,18 +6,20 @@ import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigLengthsUtil, ContigNameConversions }
 import org.hammerlab.genomics.reference.{ ContigLengths, ContigName, Locus, NumLoci }
 import org.hammerlab.spark.test.suite.KryoSparkSuite
+import org.hammerlab.kryo._
 
 import scala.collection.mutable
 
 class LociSetSuite
-  extends KryoSparkSuite(classOf[Registrar])
+  extends KryoSparkSuite
     with LociSetUtil
     with ContigNameConversions
     with ClearContigNames
     with ContigLengthsUtil {
 
   // "loci set invariants" collects some LociSets
   register(
+    arr[LociSet],
     classOf[mutable.WrappedArray.ofRef[_]]
   )
 

src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala

@@ -8,12 +8,13 @@ import org.hammerlab.genomics.reference.ContigName.Factory
 import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.genomics.reference.test.{ ClearContigNames, LenientContigNameConversions }
 import org.hammerlab.genomics.reference.{ Locus, PermissiveRegistrar }
+import org.hammerlab.kryo._
 import org.hammerlab.spark.test.suite.{ KryoSparkSuite, SparkSerialization }
 
 import scala.collection.mutable
 
 class SerializerSuite
-  extends KryoSparkSuite(classOf[Registrar], referenceTracking = true)
+  extends KryoSparkSuite(referenceTracking = true)
     with SparkSerialization
     with LenientContigNameConversions
     with ClearContigNames
@@ -23,14 +24,16 @@ class SerializerSuite
   import Helpers._
 
   register(
+    arr[LociSet],
+
     // "a closure that includes a LociSet" parallelizes some Range[Long]s.
-    classOf[Range],
-    classOf[Array[Locus]],
+    cls[Range],
+    cls[Array[Locus]],
 
     // "make an RDD[LociSet] and an RDD[Contig]" collects some Strings.
-    classOf[Array[String]],
+    cls[Array[String]],
 
-    classOf[mutable.WrappedArray.ofRef[_]],
+    cls[mutable.WrappedArray.ofRef[_]],
 
     PermissiveRegistrar
   )