Merge pull request #14 from ryan-williams/deps

upgrade reference, test deps
hammerlab · Mar 13, 2017 · b211dfa · b211dfa
2 parents 640b783 + ca52ba3
commit b211dfa
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Showing 17 changed files with 70 additions and 60 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -5,7 +5,6 @@ jdk:
   - oraclejdk8
 
 scala:
-  - 2.10.6
   - 2.11.8
 
 script: sbt ++$TRAVIS_SCALA_VERSION clean test

diff --git a/build.sbt b/build.sbt
@@ -1,7 +1,7 @@
 
 organization := "org.hammerlab.genomics"
 name := "loci"
-version := "1.5.2"
+version := "1.5.3"
 
 addSparkDeps
 

diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.6.3")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.7.1")
diff --git a/src/main/scala/org/hammerlab/genomics/loci/VariantContext.scala b/src/main/scala/org/hammerlab/genomics/loci/VariantContext.scala
@@ -8,8 +8,8 @@ object VariantContext {
     Some(
       (
         vc.getContig,
-        vc.getStart - 1L,
-        vc.getEnd.toLong
+        Locus(vc.getStart - 1L),
+        Locus(vc.getEnd.toLong)
       )
     )
 }
diff --git a/src/main/scala/org/hammerlab/genomics/loci/map/Contig.scala b/src/main/scala/org/hammerlab/genomics/loci/map/Contig.scala
@@ -37,7 +37,7 @@ case class Contig[T](name: ContigName, private val rangeMap: RangeMap[Locus, T])
   def getAll(start: Locus, end: Locus): Set[T] = getAll(start, end, halfWindowSize = 0)
   def getAll(start: Locus, end: Locus, halfWindowSize: Int): Set[T] =
     rangeMap
-      .subRangeMap(lociRange(start.locus - halfWindowSize, end.locus + halfWindowSize))
+      .subRangeMap(lociRange(start - halfWindowSize, end + halfWindowSize))
       .asMapOfRanges
       .values
       .toSet

diff --git a/src/main/scala/org/hammerlab/genomics/loci/parsing/LociRange.scala b/src/main/scala/org/hammerlab/genomics/loci/parsing/LociRange.scala
@@ -38,12 +38,12 @@ object ParsedLociRange {
       case "none" | "" =>
         None
       case contigAndLoci(name, startStr, endStrOpt) =>
-        val start = startStr.toLong
+        val start = Locus(startStr.toLong)
         val endOpt: Option[Locus] =
           Option(endStrOpt) match {
             case Some("") => None
-            case Some(s) => Some(s.toLong)
-            case None => Some(start + 1)
+            case Some(s) => Some(Locus(s.toLong))
+            case None => Some(start.next)
           }
 
         Some(LociRange(name, start, endOpt))

diff --git a/src/main/scala/org/hammerlab/genomics/loci/set/Contig.scala b/src/main/scala/org/hammerlab/genomics/loci/set/Contig.scala
@@ -25,8 +25,8 @@ case class Contig(var name: ContigName, private var rangeSet: RangeSet[Locus]) e
     for {
       i <- 0 until num
     } {
-      val start = in.readLong()
-      val end = in.readLong()
+      val start = Locus(in.readLong())
+      val end = Locus(in.readLong())
       val range = lociRange(start, end)
       rangeSet.add(range)
     }
@@ -65,7 +65,7 @@ case class Contig(var name: ContigName, private var rangeSet: RangeSet[Locus]) e
   def iterator = new LociIterator(ranges.iterator.buffered)
 
   /** Number of loci on this contig. */
-  def count: NumLoci = ranges.map(_.length: Long).sum
+  def count: NumLoci = ranges.map(_.length).sum
 
   /** Returns whether a given genomic region overlaps with any loci on this contig. */
   def intersects(start: Locus, end: Locus): Boolean = !rangeSet.subRangeSet(lociRange(start, end)).isEmpty
@@ -75,7 +75,7 @@ case class Contig(var name: ContigName, private var rangeSet: RangeSet[Locus]) e
    *
    * Used by LociSet.take.
    */
-  private[set] def take(numToTake: Long): (Contig, Contig) = {
+  private[set] def take(numToTake: NumLoci): (Contig, Contig) = {
     val firstRanges = ArrayBuffer[Interval]()
     val secondRanges = ArrayBuffer[Interval]()
 

diff --git a/src/main/scala/org/hammerlab/genomics/loci/set/ContigSerializer.scala b/src/main/scala/org/hammerlab/genomics/loci/set/ContigSerializer.scala
@@ -3,6 +3,7 @@ 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 JRange.closedOpen
 import org.hammerlab.genomics.reference.{ ContigName, Interval, Locus }
 
 // We serialize a LociSet simply by writing out its constituent Contigs.
@@ -12,7 +13,7 @@ class ContigSerializer extends KryoSerializer[Contig] {
     kryo.writeObject(output, obj.name)
     output.writeInt(obj.ranges.length)
     for {
-      Interval(start, end) <- obj.ranges
+      Interval(start, end) ← obj.ranges
     } {
       output.writeLong(start.locus)
       output.writeLong(end.locus)
@@ -23,8 +24,13 @@ class ContigSerializer extends KryoSerializer[Contig] {
     val name = kryo.readObject(input, classOf[ContigName])
     val length = input.readInt()
     val treeRangeSet = TreeRangeSet.create[Locus]()
-    val ranges = (0 until length).foreach { _ =>
-      treeRangeSet.add(JRange.closedOpen[Locus](input.readLong(), input.readLong()))
+    val ranges = (0 until length).foreach { _ ⇒
+      treeRangeSet.add(
+        closedOpen(
+          Locus(input.readLong()),
+          Locus(input.readLong())
+        )
+      )
     }
     Contig(name, treeRangeSet)
   }

diff --git a/src/main/scala/org/hammerlab/genomics/loci/set/LociSet.scala b/src/main/scala/org/hammerlab/genomics/loci/set/LociSet.scala
@@ -147,9 +147,9 @@ object LociSet {
       .map(Contig(_))
     )
 
-  def apply(ranges: ParsedLoci, contigLengths: ContigLengths): LociSet =
+  def apply(loci: ParsedLoci, contigLengths: ContigLengths): LociSet =
     LociSet(
-      ranges match {
+      loci match {
         case All =>
           for {
             (contig, length) <- contigLengths

diff --git a/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala
@@ -24,7 +24,7 @@ class SkippableLociIteratorSuite
     )
 
   test("no skips") {
-    strs.toList should ===(
+    strs.toSeq should ===(
       List(
         10 → "a",
         11 → "b",
@@ -76,8 +76,8 @@ class SkippableLociIteratorSuite
           Interval(50, 51)
         ).buffered
       )
-    ).toList ===
-      List(
+    ).toSeq ===
+      Seq(
         10 → "a",
         30 → "e",
         31 → "f",

diff --git a/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala
@@ -2,13 +2,13 @@ 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.{ ClearContigNames, ContigNameConversions }
 import org.hammerlab.genomics.reference.test.LociConversions._
-import org.hammerlab.genomics.reference.test.ContigNameConversions._
+import org.hammerlab.test.Suite
 
 class ContigSuite
   extends Suite
+    with ContigNameConversions
     with ClearContigNames {
 
   test("empty") {

diff --git a/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala
@@ -3,11 +3,12 @@ package org.hammerlab.genomics.loci.map
 import org.hammerlab.genomics.loci.set.test.LociSetUtil
 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.genomics.reference.test.ContigNameConversions
 import org.hammerlab.test.Suite
 
 class LociMapSuite
   extends Suite
+    with ContigNameConversions
     with LociSetUtil {
 
   test("properties of empty LociMap") {

diff --git a/src/test/scala/org/hammerlab/genomics/loci/map/SerializerSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/map/SerializerSuite.scala
@@ -35,31 +35,31 @@ class SerializerSuite
   testSerde("empty")()(9, 0, 0)
 
   testSerde("1")(
-    ("chr1", 100L, 200L, "A")
+    ("chr1", 100, 200, "A")
   )(
     40, 1, 100
   )
 
   testSerde("2")(
-    ("chr1", 100L, 200L, "A"),
-    ("chr1", 400L, 500L, "B")
+    ("chr1", 100, 200, "A"),
+    ("chr1", 400, 500, "B")
   )(
     59, 2, 200
   )
 
   testSerde("3")(
-    ("chr1", 100L, 200L, "A"),
-    ("chr1", 400L, 500L, "B"),
-    ("chr1", 600L, 700L, "C")
+    ("chr1", 100, 200, "A"),
+    ("chr1", 400, 500, "B"),
+    ("chr1", 600, 700, "C")
   )(
     78, 3, 300
   )
 
   testSerde("4")(
-    ("chr1", 100L, 200L, "A"),
-    ("chr1", 400L, 500L, "B"),
-    ("chr1", 600L, 700L, "C"),
-    ("chr1", 700L, 800L, "A")
+    ("chr1", 100, 200, "A"),
+    ("chr1", 400, 500, "B"),
+    ("chr1", 600, 700, "C"),
+    ("chr1", 700, 800, "A")
   )(
     97, 4, 400
   )

diff --git a/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala
@@ -20,7 +20,7 @@ class ParsedLociSuite
       lociSet(
         ParsedLoci.fromArgs(
           lociStrOpt = None,
-          lociFileOpt = Some(File("truth.chr20.vcf").path),
+          lociFileOpt = Some(File("truth.chr20.vcf")),
           conf
         ).get
       )

diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala
@@ -10,7 +10,7 @@ class LociIteratorSuite extends Suite {
   def loci(intervals: (Int, Int)*): LociIterator =
     new LociIterator(
       (for {
-        (start, end) <- intervals
+        (start, end) ← intervals
       } yield
         Interval(start, end)
       )
@@ -19,17 +19,17 @@ class LociIteratorSuite extends Suite {
     )
 
   test("simple") {
-    loci(100 -> 110).toList should ===(100 until 110)
+    loci(100 → 110).toSeq should ===(100 until 110)
   }
 
   test("skipTo") {
     val it = loci(100 -> 110)
     it.skipTo(103)
     it.head should ===(103)
-    it.toList should ===(103 until 110)
+    it.toSeq should ===(103 until 110)
   }
 
   test("intervals") {
-    loci(100 -> 110, 120 -> 130).toList should ===((100 until 110) ++ (120 until 130))
+    loci(100 → 110, 120 → 130).toSeq should ===((100 until 110) ++ (120 until 130))
   }
 }
diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/LociSetSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/LociSetSuite.scala
@@ -2,24 +2,25 @@ 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.{ 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.genomics.reference.test.{ ClearContigNames, ContigLengthsUtil, LenientContigNameConversions }
+import org.hammerlab.genomics.reference.test.LociConversions._
+import org.hammerlab.genomics.reference.{ ContigLengths, ContigName, Locus, NumLoci, PermissiveRegistrar }
 import org.hammerlab.spark.test.suite.KryoSparkSuite
 
 import scala.collection.mutable
 
 class LociSetSuite
   extends KryoSparkSuite(classOf[Registrar])
     with LociSetUtil
+    with LenientContigNameConversions
     with ClearContigNames
     with ContigLengthsUtil {
 
-  import org.hammerlab.genomics.reference.ContigName.Normalization.Lenient
-
   // "loci set invariants" collects some LociSets
-  register(classOf[mutable.WrappedArray.ofRef[_]])
+  register(
+    classOf[mutable.WrappedArray.ofRef[_]],
+    PermissiveRegistrar
+  )
 
   def makeLociSet(str: String, lengths: (ContigName, NumLoci)*): LociSet =
     LociSet(ParsedLoci(str), lengths.toMap)
@@ -160,17 +161,20 @@ class LociSetSuite
     iter1.next() should ===(2)
     iter1.next() should ===(10)
     iter1.next() should ===(11)
-    iter1.skipTo(6000000000L)  // will hang if it steps through each locus.
-    iter1.next() should ===(6000000000L)
-    iter1.next() should ===(6000000001L)
+
+    val sixBillion = Locus(6000000000L)
+    iter1.skipTo(sixBillion)  // will hang if it steps through each locus.
+    iter1.next() should ===(sixBillion)
+    iter1.next() should ===(sixBillion.next)
     iter1.hasNext should ===(true)
 
+    val hundredBillion = Locus(100000000000L)
     val iter2 = set("chr1").iterator
-    iter2.skipTo(100000000000L)
+    iter2.skipTo(hundredBillion)
     iter2.hasNext should ===(false)
 
     val iter3 = set("chr1").iterator
-    iter3.skipTo(100000000000L - 1)
+    iter3.skipTo(hundredBillion.prev)
     iter3.hasNext should ===(true)
     iter3.next() should ===(100000000000L - 1)
     iter3.hasNext should ===(false)

diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala
@@ -5,22 +5,22 @@ import java.io.{ ByteArrayInputStream, ByteArrayOutputStream, ObjectInputStream,
 import org.apache.spark.broadcast.Broadcast
 import org.hammerlab.genomics.loci.set.test.LociSetUtil
 import org.hammerlab.genomics.reference.ContigName.Factory
-import org.hammerlab.genomics.reference.Locus
-import org.hammerlab.genomics.reference.test.ClearContigNames
-import org.hammerlab.genomics.reference.test.LociConversions.{ intToLocus, toArray, toSeq }
+import org.hammerlab.genomics.reference.{ Locus, PermissiveRegistrar }
+import org.hammerlab.genomics.reference.test.{ ClearContigNames, LenientContigNameConversions }
+import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.spark.test.suite.{ KryoSparkSuite, SparkSerialization }
 
 import scala.collection.mutable
 
 class SerializerSuite
   extends KryoSparkSuite(classOf[Registrar], referenceTracking = true)
     with SparkSerialization
+    with LenientContigNameConversions
     with ClearContigNames
     with LociSetUtil
     with Serializable {
 
   import Helpers._
-  import org.hammerlab.genomics.reference.ContigName.Normalization.Lenient
 
   // "a closure that includes a LociSet" parallelizes some Range[Long]s.
   register(
@@ -30,11 +30,12 @@ class SerializerSuite
     // "make an RDD[LociSet] and an RDD[Contig]" collects some Strings.
     classOf[Array[String]],
 
-    classOf[mutable.WrappedArray.ofRef[_]]
+    classOf[mutable.WrappedArray.ofRef[_]],
+
+    PermissiveRegistrar
   )
 
   test("make an RDD[LociSet]") {
-    import org.hammerlab.genomics.reference.ContigName.Normalization.Lenient
     val sets =
       List[LociSet](
         "",
@@ -52,7 +53,6 @@ class SerializerSuite
   }
 
   test("make an RDD[LociSet], and an RDD[Contig]") {
-    import org.hammerlab.genomics.reference.ContigName.Normalization.Lenient
     val sets =
       List[LociSet](
         "",
@@ -77,7 +77,7 @@ class SerializerSuite
   test("a closure that includes a LociSet") {
     val set: LociSet = "chr21:100-200,chr20:0-10,chr20:8-15,chr20:100-120,empty:10-10"
     val setBC = sc.broadcast(set)
-    val rdd = sc.parallelize[Locus](0 until 1000)
+    val rdd = sc.parallelize[Locus]((0 until 1000).toSeq)
     val result = rdd.filter(lociSetFilterTask(setBC)).collect
     result should ===(100 until 200)
   }