Cleaning up org.bdgenomics.adam.rdd.ADAMContext:

* Made constructor private.
* Removed dead implicits.
* Made `loadParquet` package private.
* Broke long lines.
* Added scaladoc.
* Removed non-ideomatic uses of `Option`s.
* Removed unused overloaded `loadFeatures` definition.
* Removed `loadGenes` and `PrintGenes` command.
* Added support for .vcf.gz in `loadGenotypes` and `loadVariants`.

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

@@ -40,29 +40,13 @@ object JavaADAMContext {
   implicit def toADAMContext(jac: JavaADAMContext): ADAMContext = jac.ac
 }
 
-class JavaADAMContext(val ac: ADAMContext) extends Serializable {
+class JavaADAMContext private (val ac: ADAMContext) extends Serializable {
 
   /**
    * @return Returns the Java Spark Context associated with this Java ADAM Context.
    */
   def getSparkContext: JavaSparkContext = new JavaSparkContext(ac.sc)
 
-  /**
-   * Builds this Java ADAM Context using an existing Java Spark Context.
-   *
-   * @param jsc Java Spark Context to use to build this ADAM Context.
-   * @return A new Java ADAM Context.
-   */
-  def this(jsc: JavaSparkContext) = this(new ADAMContext(jsc))
-
-  /**
-   * Builds this Java ADAM Context using an existing Spark Context.
-   *
-   * @param sc Spark Context to use to build this ADAM Context.
-   * @return A new Java ADAM Context.
-   */
-  def this(sc: SparkContext) = this(new ADAMContext(sc))
-
   /**
    * Loads in an ADAM read file. This method can load SAM, BAM, and ADAM files.
    *

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

@@ -59,7 +59,6 @@ object ADAMMain {
         "PRINT",
         List(
           PrintADAM,
-          PrintGenes,
           FlagStat,
           ListDict,
           AlleleCount,

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Features2ADAM.scala

@@ -40,14 +40,14 @@ class Features2ADAMArgs extends Args4jBase with ParquetSaveArgs {
   var outputPath: String = null
   @Args4jOption(required = false, name = "-num_partitions",
     usage = "Number of partitions to load an interval file using.")
-  var numPartitions: Int = 10
+  var numPartitions: Int = _
 }
 
 class Features2ADAM(val args: Features2ADAMArgs)
     extends BDGSparkCommand[Features2ADAMArgs] {
   val companion = Features2ADAM
 
   def run(sc: SparkContext) {
-    sc.loadFeatures(args.featuresFile, None, args.numPartitions).saveAsParquet(args)
+    sc.loadFeatures(args.featuresFile, None, Option(args.numPartitions)).saveAsParquet(args)
   }
 }