[ADAM-1417] Removed unused Projection.apply method, add test for Filter.

Resolves #1417.

adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala

@@ -38,8 +38,8 @@ object Projection {
   private def createFilterPredicate(fieldNames: Set[String],
                                     exclude: Boolean = false): Field => Boolean = {
     val filterPred = (f: Field) => fieldNames.contains(f.name)
-    val includeOrExlcude = (contains: Boolean) => if (exclude) !contains else contains
-    filterPred.andThen(includeOrExlcude)
+    val includeOrExclude = (contains: Boolean) => if (exclude) !contains else contains
+    filterPred.andThen(includeOrExclude)
   }
 
   /**
@@ -60,25 +60,6 @@ object Projection {
     Projection(false, includedFields: _*)
   }
 
-  /**
-   * Creates a projection that includes a variable number of fields.
-   *
-   * @param includedFields Fields to include in the projection
-   * @return Returns the specified schema with the fields predicated out.
-   *
-   * @note The schema is inferred from the provided FieldValues. Undefined
-   *   behavior may result if you provide FieldValues from multiple different
-   *   FieldEnumerations.
-   *
-   * @throws IllegalArgumentException if there are no fields included in the
-   *   projection.
-   */
-  def apply(includedFields: Traversable[FieldValue]): Schema = {
-    require(includedFields.size > 0, "Can't project down to zero fields!")
-    val baseSchema = includedFields.head.schema
-    createProjection(baseSchema, includedFields.map(_.toString).toSet, false)
-  }
-
   /**
    * Creates a projection that either includes or excludes a variable number of
    * fields.

adam-core/src/test/scala/org/bdgenomics/adam/projections/AlignmentRecordFieldSuite.scala

@@ -75,4 +75,20 @@ class AlignmentRecordFieldSuite extends ADAMFunSuite {
     assert(alignmentRecords.first.getContigName === "6")
     assert(alignmentRecords.first.getStart === 29941260L)
   }
+
+  sparkTest("filter contigName when reading parquet alignment records") {
+    val path = tmpFile("alignmentRecords.parquet")
+    val rdd = sc.parallelize(Seq(AlignmentRecord.newBuilder()
+      .setContigName("6")
+      .setStart(29941260L)
+      .build()))
+    rdd.saveAsParquet(TestSaveArgs(path))
+
+    val projection = Filter(contigName)
+
+    val alignmentRecords: RDD[AlignmentRecord] = sc.loadParquet(path, optProjection = Some(projection))
+    assert(alignmentRecords.count() === 1)
+    assert(alignmentRecords.first.getContigName == null)
+    assert(alignmentRecords.first.getStart === 29941260L)
+  }
 }