Merge pull request #21 from ryan-williams/h

upgrade plugin, spark
hammerlab · Aug 6, 2017 · 5735f94 · 5735f94
2 parents c51cd7a + 1f0523a
commit 5735f94
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Showing 6 changed files with 47 additions and 62 deletions.
diff --git a/build.sbt b/build.sbt
@@ -1,28 +1,28 @@
 
 organization := "org.hammerlab.genomics"
 name := "loci"
-version := "1.5.8"
+version := "2.0.0"
 
 addSparkDeps
 
 deps ++= Seq(
-  libs.value('args4j),
-  libs.value('args4s),
-  libs.value('htsjdk),
-  libs.value('iterators),
-  libs.value('paths),
-  libs.value('scalautils),
-  libs.value('string_utils)
+  args4j,
+  "org.hammerlab" ^^ "args4s" ^ "1.3.0",
+  htsjdk,
+  iterators % "1.3.0",
+  paths % "1.2.0",
+  scalautils,
+  string_utils % "1.2.0"
 )
 
-compileAndTestDeps += libs.value('reference)
+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 += "com.google.guava" % "guava" % "19.0"
+shadedDeps += guava
 
 // Rename shaded Guava classes.
-shadeRenames += "com.google.common.**" -> "org.hammerlab.guava.@1"
-shadeRenames += "com.google.thirdparty.**" -> "org.hammerlab.guava.@1"
+shadeRenames += "com.google.common.**" → "org.hammerlab.guava.@1"
+shadeRenames += "com.google.thirdparty.**" → "org.hammerlab.guava.@1"
 
 // Publish JAR that includes shaded Guava.
 publishThinShadedJar

diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "2.0.1")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.0.0")
diff --git a/src/main/scala/org/hammerlab/genomics/loci/iterator/MergeLociIterator.scala b/src/main/scala/org/hammerlab/genomics/loci/iterator/MergeLociIterator.scala
diff --git a/src/main/scala/org/hammerlab/genomics/loci/parsing/ParsedLoci.scala b/src/main/scala/org/hammerlab/genomics/loci/parsing/ParsedLoci.scala
@@ -1,7 +1,6 @@
 package org.hammerlab.genomics.loci.parsing
 
 import htsjdk.variant.vcf.VCFFileReader
-import org.apache.hadoop.conf.Configuration
 import org.hammerlab.genomics.loci.VariantContext
 import org.hammerlab.genomics.loci.args.LociArgs
 import org.hammerlab.genomics.reference.ContigName.Factory
@@ -56,16 +55,17 @@ object ParsedLoci {
    * (lociFileOpt), and return a [[ParsedLoci]] encapsulating the result. The latter can then be converted into a
    * [[org.hammerlab.genomics.loci.set.LociSet]] when contig-lengths are available / have been parsed from read-sets.
    */
-  def apply(args: LociArgs,
-            hadoopConfiguration: Configuration): Option[ParsedLoci] =
-    apply(args.lociStrOpt, args.lociFileOpt, hadoopConfiguration)
+  def apply(args: LociArgs): Option[ParsedLoci] =
+    apply(
+      args.lociStrOpt,
+      args.lociFileOpt
+    )
 
   def apply(lociStrOpt: Option[String],
-            lociFileOpt: Option[Path],
-            hadoopConfiguration: Configuration)(implicit factory: Factory): Option[ParsedLoci] =
+            lociFileOpt: Option[Path])(implicit factory: Factory): Option[ParsedLoci] =
     (lociStrOpt, lociFileOpt) match {
       case (Some(lociStr), _) => Some(ParsedLoci(lociStr))
-      case (_, Some(lociPath)) => Some(loadFromPath(lociPath, hadoopConfiguration))
+      case (_, Some(lociPath)) => Some(loadFromPath(lociPath))
       case _ =>
         None
     }
@@ -78,8 +78,7 @@ object ParsedLoci {
    *                 "chrX:5-10,chr12-10-20", etc. Whitespace is ignored.
    * @return parsed loci
    */
-  private def loadFromPath(path: Path,
-                           hadoopConfiguration: Configuration)(implicit factory: Factory): ParsedLoci =
+  private def loadFromPath(path: Path)(implicit factory: Factory): ParsedLoci =
     path.extension match {
       case "vcf" ⇒ LociRanges.fromVCF(path)
       case "loci" | "txt" ⇒ ParsedLoci(path.lines)

diff --git a/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala
@@ -1,6 +1,5 @@
 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.ClearContigNames
 import org.hammerlab.genomics.reference.test.LociConversions.intToLocus
@@ -12,16 +11,13 @@ class ParsedLociSuite
     with ClearContigNames
     with LociSetUtil {
 
-  val conf = new Configuration
-
   // Loci-from-VCF sanity check.
   test("vcf loading") {
     val loci =
       lociSet(
         ParsedLoci(
           lociStrOpt = None,
-          lociFileOpt = Some(File("truth.chr20.vcf").path),
-          conf
+          lociFileOpt = Some(File("truth.chr20.vcf").path)
         ).get
       )
 

diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/LociSetSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/LociSetSuite.scala
@@ -178,4 +178,29 @@ class LociSetSuite
     iter3.next() should ===(100000000000L - 1)
     iter3.hasNext should ===(false)
   }
+
+  test("take") {
+    val set = lociSet("chr1:100-200,chr2:30-40,chr3:50-51,chr4:1000-1100")
+
+    set.take(10) should be(
+      (
+        lociSet("chr1:100-110"),
+        lociSet("chr1:110-200,chr2:30-40,chr3:50-51,chr4:1000-1100")
+      )
+    )
+
+    set.take(0) should be(
+      (
+        lociSet(""),
+        set
+      )
+    )
+
+    set.take(200) should be(
+      (
+        lociSet("chr1:100-200,chr2:30-40,chr3:50-51,chr4:1000-1089"),
+        lociSet("chr4:1089-1100")
+      )
+    )
+  }
 }