use ContigName factories

build.sbt

@@ -1,7 +1,7 @@
 
 organization := "org.hammerlab.genomics"
 name := "loci"
-version := "1.5.0"
+version := "1.5.1-SNAPSHOT"
 
 addSparkDeps
 

project/plugins.sbt

@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.5.6")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.5.8-SNAPSHOT")

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

@@ -2,14 +2,14 @@ package org.hammerlab.genomics.loci.map
 
 import com.esotericsoftware.kryo.io.{ Input, Output }
 import com.esotericsoftware.kryo.{ Kryo, Serializer ⇒ KryoSerializer }
-import org.hammerlab.genomics.reference.Locus
+import org.hammerlab.genomics.reference.{ ContigName, Locus }
 
 /**
  * We serialize a Contig as its name, the number of ranges, and the ranges themselves (two longs and a value each).
  */
 class ContigSerializer[T] extends KryoSerializer[Contig[T]] {
   def write(kryo: Kryo, output: Output, obj: Contig[T]) = {
-    output.writeString(obj.name.name)
+    kryo.writeObject(output, obj.name)
     output.writeLong(obj.asMap.size)
     obj.asMap.foreach {
       case (range, value) =>
@@ -21,7 +21,7 @@ class ContigSerializer[T] extends KryoSerializer[Contig[T]] {
 
   def read(kryo: Kryo, input: Input, klass: Class[Contig[T]]): Contig[T] = {
     val builder = LociMap.newBuilder[T]
-    val contig = input.readString()
+    val contig = kryo.readObject(input, classOf[ContigName])
     val count = input.readLong()
     (0L until count).foreach { _ =>
       val start = input.readLong()

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

@@ -2,9 +2,12 @@ package org.hammerlab.genomics.loci.map
 
 import com.esotericsoftware.kryo.Kryo
 import org.apache.spark.serializer.KryoRegistrator
+import org.hammerlab.genomics.reference
 
 class Registrar extends KryoRegistrator {
   override def registerClasses(kryo: Kryo): Unit = {
+    new reference.Registrar().registerClasses(kryo)
+
     kryo.register(classOf[LociMap[_]], new Serializer)
     kryo.register(classOf[Array[LociMap[_]]])
     kryo.register(classOf[Contig[_]], new ContigSerializer)

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

@@ -1,7 +1,7 @@
 package org.hammerlab.genomics.loci.map
 
-import com.esotericsoftware.kryo.io.{Input, Output}
-import com.esotericsoftware.kryo.{Kryo, Serializer => KryoSerializer}
+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.

src/main/scala/org/hammerlab/genomics/loci/parsing/LociRange.scala

@@ -1,6 +1,7 @@
 package org.hammerlab.genomics.loci.parsing
 
-import org.hammerlab.genomics.reference.{ContigName, Locus}
+import org.hammerlab.genomics.reference.ContigName.Factory
+import org.hammerlab.genomics.reference.{ ContigName, Locus }
 
 /**
  * Representation of a genomic range as parsed from a cmdline-flag or file.
@@ -30,7 +31,7 @@ object ParsedLociRange {
    *  "chr1:10000": just chr1, position 10000; equivalent to "chr1:10000-10001".
    *  "chr1:10000-": chr1, from position 10000 to the end of chr1.
    */
-  def apply(lociRangeStr: String): Option[ParsedLociRange] =
+  def apply(lociRangeStr: String)(implicit factory: Factory): Option[ParsedLociRange] =
     lociRangeStr.replaceAll("\\s", "") match {
       case "all" =>
         Some(AllRange)

src/main/scala/org/hammerlab/genomics/loci/parsing/ParsedLoci.scala

@@ -7,6 +7,7 @@ import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.Path
 import org.hammerlab.genomics.loci.VariantContext
 import org.hammerlab.genomics.loci.args.LociArgs
+import org.hammerlab.genomics.reference.ContigName.Factory
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable.ArrayBuffer
@@ -35,11 +36,9 @@ import scala.io.Source
 sealed trait ParsedLoci extends Any
 
 object ParsedLoci {
-  val empty = apply("")
+  def apply(lociStrs: String)(implicit factory: Factory): ParsedLoci = apply(Iterator(lociStrs))
 
-  def apply(lociStrs: String): ParsedLoci = apply(Iterator(lociStrs))
-
-  def apply(lines: Iterator[String]): ParsedLoci = {
+  def apply(lines: Iterator[String])(implicit factory: Factory): ParsedLoci = {
     val lociRanges = ArrayBuffer[LociRange]()
     for {
       lociStrs <- lines
@@ -65,7 +64,7 @@ object ParsedLoci {
 
   def fromArgs(lociStrOpt: Option[String],
                lociFileOpt: Option[String],
-               hadoopConfiguration: Configuration): Option[ParsedLoci] =
+               hadoopConfiguration: Configuration)(implicit factory: Factory): Option[ParsedLoci] =
     (lociStrOpt, lociFileOpt) match {
       case (Some(lociStr), _) => Some(ParsedLoci(lociStr))
       case (_, Some(lociFile)) => Some(loadFromFile(lociFile, hadoopConfiguration))
@@ -81,7 +80,7 @@ object ParsedLoci {
    *                 "chrX:5-10,chr12-10-20", etc. Whitespace is ignored.
    * @return parsed loci
    */
-  private def loadFromFile(lociFile: String, hadoopConfiguration: Configuration): ParsedLoci =
+  private def loadFromFile(lociFile: String, hadoopConfiguration: Configuration)(implicit factory: Factory): ParsedLoci =
     if (lociFile.endsWith(".vcf")) {
       LociRanges.fromVCF(lociFile)
     } else if (lociFile.endsWith(".loci") || lociFile.endsWith(".txt")) {

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

@@ -3,12 +3,13 @@ package org.hammerlab.genomics.loci.set
 import com.esotericsoftware.kryo.io.{ Input, Output }
 import com.esotericsoftware.kryo.{ Kryo, Serializer ⇒ KryoSerializer }
 import com.google.common.collect.{ TreeRangeSet, Range ⇒ JRange }
-import org.hammerlab.genomics.reference.{ Interval, Locus }
+import org.hammerlab.genomics.reference.{ ContigName, Interval, Locus }
 
 // We serialize a LociSet simply by writing out its constituent Contigs.
 class ContigSerializer extends KryoSerializer[Contig] {
+
   def write(kryo: Kryo, output: Output, obj: Contig) = {
-    output.writeString(obj.name.name)
+    kryo.writeObject(output, obj.name)
     output.writeInt(obj.ranges.length)
     for {
       Interval(start, end) <- obj.ranges
@@ -19,12 +20,12 @@ class ContigSerializer extends KryoSerializer[Contig] {
   }
 
   def read(kryo: Kryo, input: Input, klass: Class[Contig]): Contig = {
-    val name = input.readString()
+    val name = kryo.readObject(input, classOf[ContigName])
     val length = input.readInt()
     val treeRangeSet = TreeRangeSet.create[Locus]()
-    val ranges = (0 until length).foreach(_ => {
+    val ranges = (0 until length).foreach { _ =>
       treeRangeSet.add(JRange.closedOpen[Locus](input.readLong(), input.readLong()))
-    })
+    }
     Contig(name, treeRangeSet)
   }
 }

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

@@ -26,7 +26,7 @@ case class LociSet(private val map: SortedMap[ContigName, Contig]) extends Trunc
   @transient lazy val contigs = map.values.toArray
 
   /** The number of loci in this LociSet. */
-  @transient lazy val count: NumLoci = contigs.map(_.count: Long).sum
+  @transient lazy val count: NumLoci = contigs.map(_.count).sum
 
   def isEmpty = map.isEmpty
   def nonEmpty = map.nonEmpty

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

@@ -2,9 +2,12 @@ package org.hammerlab.genomics.loci.set
 
 import com.esotericsoftware.kryo.Kryo
 import org.apache.spark.serializer.KryoRegistrator
+import org.hammerlab.genomics.reference
 
 class Registrar extends KryoRegistrator {
   override def registerClasses(kryo: Kryo): Unit = {
+    new reference.Registrar().registerClasses(kryo)
+
     kryo.register(classOf[LociSet], new Serializer)
     kryo.register(classOf[Array[LociSet]])
     kryo.register(classOf[Contig], new ContigSerializer)

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

@@ -1,7 +1,7 @@
 package org.hammerlab.genomics.loci.set
 
-import com.esotericsoftware.kryo.io.{Input, Output}
-import com.esotericsoftware.kryo.{Kryo, Serializer => KryoSerializer}
+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] {

src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala

@@ -1,13 +1,12 @@
 package org.hammerlab.genomics.loci.iterator
 
-import org.hammerlab.genomics.reference.test.LocusUtil._
-import org.hammerlab.genomics.reference.test.{ IntervalsUtil, LocusUtil }
+import org.hammerlab.genomics.reference.test.IntervalsUtil
+import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.genomics.reference.{ Interval, Locus }
 import org.hammerlab.test.Suite
 
 class SkippableLociIteratorSuite
   extends Suite
-    with LocusUtil
     with IntervalsUtil {
 
   def strs =

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

@@ -2,10 +2,15 @@ package org.hammerlab.genomics.loci.map
 
 import com.google.common.collect.{ ImmutableRangeMap, Range }
 import org.hammerlab.genomics.reference.Locus
+import org.hammerlab.genomics.reference.test.ClearContigNames
 import org.hammerlab.test.Suite
-import org.hammerlab.genomics.reference.test.LocusUtil._
+import org.hammerlab.genomics.reference.test.LociConversions._
+import org.hammerlab.genomics.reference.test.ContigNameConversions._
+
+class ContigSuite
+  extends Suite
+    with ClearContigNames {
 
-class ContigSuite extends Suite {
   test("empty") {
     val contigMap = new Contig("chr1", ImmutableRangeMap.builder[Locus, String]().build())
 

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

@@ -1,15 +1,13 @@
 package org.hammerlab.genomics.loci.map
 
-import org.hammerlab.genomics.loci.set.LociSet
 import org.hammerlab.genomics.loci.set.test.LociSetUtil
-import org.hammerlab.genomics.reference.test.{ ContigNameUtil, LocusUtil }
-import org.hammerlab.genomics.reference.{ ContigName, Interval }
+import org.hammerlab.genomics.reference.Interval
+import org.hammerlab.genomics.reference.test.LociConversions.intToLocus
+import org.hammerlab.genomics.reference.test.ContigNameConversions.toSeq
 import org.hammerlab.test.Suite
 
 class LociMapSuite
   extends Suite
-    with LocusUtil
-    with ContigNameUtil
     with LociSetUtil {
 
   test("properties of empty LociMap") {

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

@@ -1,13 +1,12 @@
 package org.hammerlab.genomics.loci.map
 
-import org.hammerlab.genomics.reference.test.LocusUtil
+import org.hammerlab.genomics.reference.test.LociConversions.intToLocus
 import org.hammerlab.genomics.reference.{ ContigName, Locus }
 import org.hammerlab.spark.test.suite.{ KryoSparkSuite, SparkSerialization }
 
 class SerializerSuite
   extends KryoSparkSuite(classOf[Registrar])
-  with SparkSerialization
-    with LocusUtil {
+  with SparkSerialization {
 
   def testSerde(
     name: String

src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala

@@ -2,12 +2,13 @@ package org.hammerlab.genomics.loci.parsing
 
 import org.apache.hadoop.conf.Configuration
 import org.hammerlab.genomics.loci.set.test.LociSetUtil
-import org.hammerlab.genomics.reference.test.LocusUtil
+import org.hammerlab.genomics.reference.test.ClearContigNames
+import org.hammerlab.genomics.reference.test.LociConversions.intToLocus
 import org.hammerlab.test.Suite
 
 class ParsedLociSuite
   extends Suite
-    with LocusUtil
+    with ClearContigNames
     with LociSetUtil {
 
   val conf = new Configuration

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

@@ -2,9 +2,8 @@ package org.hammerlab.genomics.loci.set
 
 import org.hammerlab.genomics.loci.iterator.LociIterator
 import org.hammerlab.genomics.reference.Interval
-import org.hammerlab.genomics.reference.test.LocusUtil._
+import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.test.Suite
-import org.hammerlab.test.implicits.toList
 
 class LociIteratorSuite extends Suite {
 

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

@@ -2,21 +2,24 @@ package org.hammerlab.genomics.loci.set
 
 import org.hammerlab.genomics.loci.parsing.ParsedLoci
 import org.hammerlab.genomics.loci.set.test.LociSetUtil
-import org.hammerlab.genomics.reference.test.ContigLengthsUtil._
-import org.hammerlab.genomics.reference.test.ContigNameUtil
-import org.hammerlab.genomics.reference.test.LocusUtil._
+import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigLengthsUtil }
+import org.hammerlab.genomics.reference.test.ContigNameConversions.toArray
+import org.hammerlab.genomics.reference.test.LociConversions.{ intToLocus, toSeq }
 import org.hammerlab.genomics.reference.{ ContigLengths, ContigName, Locus, NumLoci }
 import org.hammerlab.spark.test.suite.KryoSparkSuite
 
 import scala.collection.mutable
 
 class LociSetSuite
   extends KryoSparkSuite(classOf[Registrar])
-    with ContigNameUtil
-    with LociSetUtil {
+    with LociSetUtil
+    with ClearContigNames
+    with ContigLengthsUtil {
+
+  import org.hammerlab.genomics.reference.ContigName.Normalization.Lenient
 
   // "loci set invariants" collects some LociSets
-  kryoRegister(classOf[mutable.WrappedArray.ofRef[_]])
+  register(classOf[mutable.WrappedArray.ofRef[_]])
 
   def makeLociSet(str: String, lengths: (ContigName, NumLoci)*): LociSet =
     LociSet(ParsedLoci(str), lengths.toMap)
@@ -65,7 +68,7 @@ class LociSetSuite
     set("chr21").intersects(90, 100) should ===(false)
     set("chr21").intersects(90, 101) should ===(true)
     set("chr21").intersects(90, 95) should ===(false)
-    set("chr21").iterator.toSeq should ===((100 until 200))
+    set("chr21").iterator.toSeq should ===(100 until 200)
   }
 
   test("single loci parsing") {
@@ -77,15 +80,17 @@ class LociSetSuite
   }
 
   test("loci set invariants") {
-    val sets = List(
-      "",
-      "empty:20-20,empty2:30-30",
-      "20:100-200",
-      "with_dots.and_underscores..2:100-200",
-      "21:300-400",
-      "X:5-17,X:19-22,Y:50-60",
-      "chr21:100-200,chr20:0-10,chr20:8-15,chr20:100-120"
-    ).map(lociSet(_))
+    val sets =
+      List(
+        "",
+        "empty:20-20,empty2:30-30",
+        "20:100-200",
+        "with_dots.and_underscores..2:100-200",
+        "21:300-400",
+        "X:5-17,X:19-22,Y:50-60",
+        "chr21:100-200,chr20:0-10,chr20:8-15,chr20:100-120"
+      )
+      .map(lociSet)
 
     def checkInvariants(set: LociSet): Unit = {
       set should not be null
@@ -103,6 +108,7 @@ class LociSetSuite
         result should ===(set)
       }
     }
+
     sets.foreach(checkInvariants)
   }