[ADAM-1169] Write GFF header line pragma in single file mode.

Resolves #1169.

adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala

@@ -333,11 +333,13 @@ case class FeatureRDD(rdd: RDD[Feature],
    * @param asSingleFile If true, combines all partition shards.
    * @param disableFastConcat If asSingleFile is true, disables the use of the
    *   parallel file merging engine.
+   * @param optHeaderPath If provided, the header file to include.
    */
   private def writeTextRdd[T](rdd: RDD[T],
                               outputPath: String,
                               asSingleFile: Boolean,
-                              disableFastConcat: Boolean) {
+                              disableFastConcat: Boolean,
+                              optHeaderPath: Option[String] = None) {
     if (asSingleFile) {
 
       // write rdd to disk
@@ -352,8 +354,10 @@ case class FeatureRDD(rdd: RDD[Feature],
         fs,
         new Path(outputPath),
         new Path(tailPath),
-        disableFastConcat = disableFastConcat)
+        disableFastConcat = disableFastConcat,
+        optHeaderPath = optHeaderPath.map(p => new Path(p)))
     } else {
+      assert(optHeaderPath.isEmpty)
       rdd.saveAsTextFile(outputPath)
     }
   }
@@ -390,10 +394,18 @@ case class FeatureRDD(rdd: RDD[Feature],
   def saveAsGff3(fileName: String,
                  asSingleFile: Boolean = false,
                  disableFastConcat: Boolean = false) = {
+    val optHeaderPath = if (asSingleFile) {
+      val headerPath = "%s_head".format(fileName)
+      GFF3HeaderWriter(headerPath, rdd.context)
+      Some(headerPath)
+    } else {
+      None
+    }
     writeTextRdd(rdd.map(FeatureRDD.toGff3),
       fileName,
       asSingleFile,
-      disableFastConcat)
+      disableFastConcat,
+      optHeaderPath = optHeaderPath)
   }
 
   /**

adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3HeaderWriter.scala

@@ -0,0 +1,45 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.adam.rdd.feature
+
+import org.apache.hadoop.fs.Path
+import org.apache.spark.SparkContext
+
+/**
+ * Writes the header for a GFF3 file to an otherwise empty file.
+ */
+private[feature] object GFF3HeaderWriter {
+
+  val HEADER_STRING = "##gff-version 3.2.1"
+
+  /**
+   * Writes a GFF3 Header pragma to a file.
+   *
+   * @param filePath The path to write the file to.
+   * @param sc The SparkContext, to access the Hadoop FS Configuration.
+   */
+  def apply(filePath: String,
+            sc: SparkContext) {
+    val path = new Path(filePath)
+    val fs = path.getFileSystem(sc.hadoopConfiguration)
+    val os = fs.create(path)
+    os.write(HEADER_STRING.getBytes)
+    os.write("\n".getBytes)
+    os.close()
+  }
+}

adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala

@@ -23,6 +23,7 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.util.ADAMFunSuite
 import org.bdgenomics.formats.avro.{ Feature, Strand }
 import org.scalactic.{ Equivalence, TypeCheckedTripleEquals }
+import scala.io.Source
 
 class FeatureRDDSuite extends ADAMFunSuite with TypeCheckedTripleEquals {
   implicit val strongFeatureEq = new Equivalence[Feature] {
@@ -173,6 +174,12 @@ class FeatureRDDSuite extends ADAMFunSuite with TypeCheckedTripleEquals {
     val outputPath = tempLocation(".gff3")
     expected.saveAsGff3(outputPath, asSingleFile = true)
 
+    val lines = Source.fromFile(outputPath)
+      .getLines
+      .toSeq
+    assert(lines.size > 1)
+    assert(lines.head === GFF3HeaderWriter.HEADER_STRING)
+
     val feature = expected.rdd.first
     val gff3Columns = FeatureRDD.toGff3(feature).split('\t')
     assert(gff3Columns.size === 9)

adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/GFF3HeaderWriterSuite.scala

@@ -0,0 +1,34 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.adam.rdd.feature
+
+import org.bdgenomics.adam.util.ADAMFunSuite
+import scala.io.Source
+
+class GFF3HeaderWriterSuite extends ADAMFunSuite {
+
+  sparkTest("write gff3 header pragma") {
+    val tmp = tmpFile(".gff3")
+    GFF3HeaderWriter(tmp, sc)
+    val lines = Source.fromFile(tmp)
+      .getLines
+      .toSeq
+    assert(lines.size === 1)
+    assert(lines.head === GFF3HeaderWriter.HEADER_STRING)
+  }
+}