[ADAM-475] Removed code that has migrated to bdg-utils.

adam-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala

@@ -19,7 +19,6 @@ package org.bdgenomics.adam.apis.java
 
 import org.apache.spark.SparkContext
 import org.apache.spark.api.java.JavaSparkContext
-import org.bdgenomics.adam.instrumentation.ADAMMetricsListener
 import org.bdgenomics.adam.predicates.ADAMPredicate
 import org.bdgenomics.adam.rdd.ADAMContext
 import org.bdgenomics.adam.rdd.ADAMContext._

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMCommand.scala

@@ -17,13 +17,19 @@
  */
 package org.bdgenomics.adam.cli
 
-import java.io.{ PrintStream, ByteArrayOutputStream }
-
+import java.io.{
+  ByteArrayOutputStream,
+  PrintStream,
+  PrintWriter
+}
 import org.apache.hadoop.mapreduce.Job
 import org.apache.spark.{ SparkConf, Logging, SparkContext }
-import org.bdgenomics.adam.instrumentation.ADAMMetrics
 import org.bdgenomics.adam.util.HadoopUtil
-import org.bdgenomics.utils.instrumentation.{ DurationFormatting, MetricsListener }
+import org.bdgenomics.utils.instrumentation.{
+  DurationFormatting,
+  MetricsListener,
+  RecordedMetrics
+}
 
 trait ADAMCommandCompanion {
   val commandName: String
@@ -48,7 +54,7 @@ trait ADAMSparkCommand[A <: Args4jBase] extends ADAMCommand with Logging {
 
   def run() {
     val start = System.nanoTime()
-    val metricsListener = if (args.printMetrics) Some(new MetricsListener(new ADAMMetrics())) else None
+    val metricsListener = if (args.printMetrics) Some(new MetricsListener(new RecordedMetrics())) else None
     val conf = new SparkConf().setAppName("adam: " + companion.commandName)
     if (conf.getOption("spark.master").isEmpty) {
       conf.setMaster("local[%d]".format(Runtime.getRuntime.availableProcessors()))
@@ -70,7 +76,7 @@ trait ADAMSparkCommand[A <: Args4jBase] extends ADAMCommand with Logging {
       out.println()
       out.println("Overall Duration: " + DurationFormatting.formatNanosecondDuration(totalTime))
       out.println()
-      listener.metrics.sparkMetrics.print(out)
+      listener.metrics.sparkMetrics.print(new PrintWriter(out))
       logInfo("Metrics:" + bytes.toString("UTF-8"))
     })
   }

adam-core/pom.xml

@@ -117,6 +117,10 @@
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.bdgenomics.bdg-utils</groupId>
+      <artifactId>bdg-utils-parquet</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.bdgenomics.bdg-utils</groupId>
       <artifactId>bdg-utils-metrics</artifactId>
@@ -182,14 +186,6 @@
       <artifactId>scalatest_${scala.artifact.suffix}</artifactId>
       <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>com.amazonaws</groupId>
-      <artifactId>aws-java-sdk</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.httpcomponents</groupId>
-      <artifactId>httpclient</artifactId>
-    </dependency>
   </dependencies>
   <profiles>
     <profile>