unify versions, Locus upgrades

build.sbt

@@ -3,7 +3,6 @@ organization := "org.hammerlab.genomics"
 name := "loci"
 version := "1.5.0-SNAPSHOT"
 
-scala211Only
 addSparkDeps
 
 deps ++= Seq(

src/main/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIterator.scala

@@ -10,7 +10,7 @@ abstract class SkippableLociIterator[T] extends SimpleBufferedIterator[T] {
   var locus: Locus = 0
 
   override def postNext(): Unit = {
-    locus += 1
+    locus = locus.next
   }
 
   def skipTo(newLocus: Locus): this.type = {

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

@@ -1,7 +1,8 @@
 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 }
+import org.hammerlab.genomics.reference.Locus
 
 /**
  * We serialize a Contig as its name, the number of ranges, and the ranges themselves (two longs and a value each).
@@ -12,8 +13,8 @@ class ContigSerializer[T] extends KryoSerializer[Contig[T]] {
     output.writeLong(obj.asMap.size)
     obj.asMap.foreach {
       case (range, value) =>
-        output.writeLong(range.start)
-        output.writeLong(range.end)
+        output.writeLong(range.start.locus)
+        output.writeLong(range.end.locus)
         kryo.writeClassAndObject(output, value)
     }
   }
@@ -26,7 +27,7 @@ class ContigSerializer[T] extends KryoSerializer[Contig[T]] {
       val start = input.readLong()
       val end = input.readLong()
       val value: T = kryo.readClassAndObject(input).asInstanceOf[T]
-      builder.put(contig, start, end, value)
+      builder.put(contig, Locus(start), Locus(end), value)
     }
     builder.result.onContig(contig)
   }

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

@@ -37,8 +37,8 @@ case class Contig(var name: ContigName, private var rangeSet: RangeSet[Locus]) e
     for {
       Interval(start, end) <- ranges
     } {
-      out.writeLong(start)
-      out.writeLong(end)
+      out.writeLong(start.locus)
+      out.writeLong(end.locus)
     }
   }
 
@@ -67,7 +67,7 @@ case class Contig(var name: ContigName, private var rangeSet: RangeSet[Locus]) e
   def count: NumLoci = ranges.map(_.length: Long).sum
 
   /** Returns whether a given genomic region overlaps with any loci on this contig. */
-  def intersects(start: Long, end: Long): Boolean = !rangeSet.subRangeSet(lociRange(start, end)).isEmpty
+  def intersects(start: Locus, end: Locus): Boolean = !rangeSet.subRangeSet(lociRange(start, end)).isEmpty
 
   /**
    * Make two new Contigs: one with the first @numToTake loci from this Contig, and the second with the rest.

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

@@ -13,8 +13,8 @@ class ContigSerializer extends KryoSerializer[Contig] {
     for {
       Interval(start, end) <- obj.ranges
     } {
-      output.writeLong(start)
-      output.writeLong(end)
+      output.writeLong(start.locus)
+      output.writeLong(end.locus)
     }
   }
 

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

@@ -99,8 +99,8 @@ case class LociSet(private val map: SortedMap[ContigName, Contig]) extends Trunc
             .map(interval =>
               new HTSJDKInterval(
                 contig.name,
-                interval.start.toInt + 1,
-                interval.end.toInt
+                interval.start.locus.toInt + 1,
+                interval.end.locus.toInt
               )
           )
       )

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

@@ -2,9 +2,12 @@ package org.hammerlab.genomics.loci.map
 
 import org.hammerlab.genomics.loci.set.test.TestLociSet
 import org.hammerlab.genomics.reference.Interval
+import org.hammerlab.genomics.reference.test.LocusUtil
 import org.hammerlab.test.Suite
 
-class LociMapSuite extends Suite {
+class LociMapSuite
+  extends Suite
+    with LocusUtil {
 
   test("properties of empty LociMap") {
     val emptyMap = LociMap[String]()
@@ -16,8 +19,8 @@ class LociMapSuite extends Suite {
 
   test("basic map operations") {
     val lociMap = LociMap(
-      ("chr1",  100L, 200L, "A"),
-      ("chr20", 200L, 201L, "B")
+      ("chr1",  100, 200, "A"),
+      ("chr20", 200, 201, "B")
     )
 
     lociMap.count === 101
@@ -39,9 +42,9 @@ class LociMapSuite extends Suite {
 
   test("asInverseMap with repeated values") {
     val lociMap = LociMap(
-      ("chr1", 100L, 200L, "A"),
-      ("chr2", 200L, 300L, "A"),
-      ("chr3", 400L, 500L, "B")
+      ("chr1", 100, 200, "A"),
+      ("chr2", 200, 300, "A"),
+      ("chr3", 400, 500, "B")
     )
 
     // asInverseMap stuffs all Loci with the same value into a LociSet.
@@ -58,30 +61,29 @@ class LociMapSuite extends Suite {
 
   test("range coalescing") {
     val lociMap = LociMap(
-      ("chr1", 100L, 200L, "A"),
-      ("chr1", 400L, 500L, "B"),
-      ("chr1", 150L, 160L, "C"),
-      ("chr1", 180L, 240L, "A")
+      ("chr1", 100, 200, "A"),
+      ("chr1", 400, 500, "B"),
+      ("chr1", 150, 160, "C"),
+      ("chr1", 180, 240, "A")
     )
 
-    lociMap.inverse === (
+    lociMap.inverse ===
       Map(
         "A" -> TestLociSet("chr1:100-150,chr1:160-240"),
         "B" -> TestLociSet("chr1:400-500"),
         "C" -> TestLociSet("chr1:150-160")
       )
-    )
 
     lociMap.count === 240
     lociMap.toString === "chr1:100-150=A,chr1:150-160=C,chr1:160-240=A,chr1:400-500=B"
   }
 
   test("spanning equal values merges") {
     val map = LociMap(
-      ("chr1", 100L, 200L, "A"),
-      ("chr1", 400L, 500L, "B"),
-      ("chr1", 300L, 400L, "A"),
-      ("chr1", 199L, 301L, "A")
+      ("chr1", 100, 200, "A"),
+      ("chr1", 400, 500, "B"),
+      ("chr1", 300, 400, "A"),
+      ("chr1", 199, 301, "A")
     )
 
     map.inverse ===
@@ -101,25 +103,23 @@ class LociMapSuite extends Suite {
 
   test("bridging equal values merges") {
     val map = LociMap(
-      ("chr1", 100L, 200L, "A"),
-      ("chr1", 400L, 500L, "B"),
-      ("chr1", 300L, 400L, "A"),
-      ("chr1", 200L, 300L, "A")
+      ("chr1", 100, 200, "A"),
+      ("chr1", 400, 500, "B"),
+      ("chr1", 300, 400, "A"),
+      ("chr1", 200, 300, "A")
     )
 
-    map.inverse === (
+    map.inverse ===
       Map(
         "A" -> TestLociSet("chr1:100-400"),
         "B" -> TestLociSet("chr1:400-500")
       )
-    )
 
-    map.onContig("chr1").asMap === (
+    map.onContig("chr1").asMap ===
       Map(
         Interval(100, 400) -> "A",
         Interval(400, 500) -> "B"
       )
-    )
 
     map.count === 400
   }