Added additional fixes to get 2.11 compiling.

bigdatagenomics · Jan 22, 2015 · 5cc2b32 · 5cc2b32
1 parent eeb251c
commit 5cc2b32
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Showing 4 changed files with 11 additions and 14 deletions.
diff --git a/adam-cli/pom.xml b/adam-cli/pom.xml
@@ -147,16 +147,16 @@
       <artifactId>args4j</artifactId>
     </dependency>
     <dependency>
-      <groupId>org.fusesource.scalate</groupId>
-      <artifactId>scalate-core_2.10</artifactId>
+      <groupId>org.scalatra.scalate</groupId>
+      <artifactId>scalate-core_${scala.artifact.suffix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.scalatra</groupId>
-      <artifactId>scalatra-json_2.10</artifactId>
+      <artifactId>scalatra-json_${scala.artifact.suffix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.scalatra</groupId>
-      <artifactId>scalatra_2.10</artifactId>
+      <artifactId>scalatra_${scala.artifact.suffix}</artifactId>
     </dependency>
     <dependency>
       <groupId>org.scalatest</groupId>

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/VariantContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/VariantContext.scala
@@ -86,8 +86,5 @@ class VariantContext(
     val variant: RichVariant,
     val genotypes: Iterable[Genotype],
     val databases: Option[DatabaseVariantAnnotation] = None) {
-  def this(variant: RichVariant, genotypes: Iterable[Genotype], database: Option[DatabaseVariantAnnotation] = None) = {
-    this(ReferencePosition(variant), variant, genotypes, database)
-  }
 }
 
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctions.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctions.scala
@@ -65,9 +65,9 @@ class VariantContextRDDFunctions(rdd: RDD[VariantContext]) extends ADAMSequenceD
 
 class GenotypeRDDFunctions(rdd: RDD[Genotype]) extends Serializable with Logging {
   def toVariantContext(): RDD[VariantContext] = {
-    rdd.keyBy({ g => RichVariant.variantToRichVariant(g.getVariant) })
+    rdd.keyBy(_.getVariant)
       .groupByKey
-      .map { case (v: RichVariant, g) => new VariantContext(v, g, None) }
+      .map(kv => VariantContext(kv._1, kv._2))
   }
 
   /**

diff --git a/pom.xml b/pom.xml
@@ -462,18 +462,18 @@
         </exclusions>
       </dependency>
       <dependency>
-        <groupId>org.fusesource.scalate</groupId>
-        <artifactId>scalate-core_2.10</artifactId>
-        <version>1.6.1</version>
+        <groupId>org.scalatra.scalate</groupId>
+        <artifactId>scalate-core_${scala.artifact.suffix}</artifactId>
+        <version>1.7.0</version>
       </dependency>
       <dependency>
         <groupId>org.scalatra</groupId>
-        <artifactId>scalatra-json_2.10</artifactId>
+        <artifactId>scalatra-json_${scala.artifact.suffix}</artifactId>
         <version>2.3.0</version>
       </dependency>
       <dependency>
         <groupId>org.scalatra</groupId>
-        <artifactId>scalatra_2.10</artifactId>
+        <artifactId>scalatra_${scala.artifact.suffix}</artifactId>
         <version>2.3.0</version>
       </dependency>
       <dependency>