[ADAM-916] New strategy for writing header.

Resolves #916. Makes several modifications that should eliminate the header
attach issue when writing back to SAM/BAM:

* Writes the SAM/BAM header as a single file.
* Instead of trying to attach the SAM/BAM header to the output format via a
  singleton object, we pass the path to the SAM/BAM header file via the Hadoop
  configuration.
* The output format reads the header from HDFS when creating the record writer.
* At the end, once we've written the full RDD and the header file, we merge all
  via Hadoop's FsUtil.

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.scala

@@ -17,11 +17,17 @@
  */
 package org.bdgenomics.adam.rdd.read
 
-import org.seqdoop.hadoop_bam.{ SAMRecordWritable, KeyIgnoringBAMOutputFormat }
 import htsjdk.samtools.SAMFileHeader
+import hbparquet.hadoop.util.ContextUtil
+import org.apache.hadoop.fs.Path
+import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext }
 import org.apache.spark.rdd.InstrumentedOutputFormat
-import org.apache.hadoop.mapreduce.OutputFormat
 import org.bdgenomics.adam.instrumentation.Timers
+import org.seqdoop.hadoop_bam.{
+  KeyIgnoringBAMOutputFormat,
+  KeyIgnoringBAMRecordWriter,
+  SAMRecordWritable
+}
 
 object ADAMBAMOutputFormat extends Serializable {
 
@@ -76,11 +82,26 @@ class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, org
 class ADAMBAMOutputFormatHeaderLess[K]
     extends KeyIgnoringBAMOutputFormat[K] with Serializable {
 
-  setSAMHeader(ADAMBAMOutputFormat.getHeader)
   setWriteHeader(false)
+
+  override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
+    val conf = ContextUtil.getConfiguration(context)
+
+    // where is our header file?
+    val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))
+
+    // read the header file
+    readSAMHeaderFrom(path, conf)
+
+    // now that we have the header set, we need to make a record reader
+    return new KeyIgnoringBAMRecordWriter[K](getDefaultWorkFile(context, ""),
+      header,
+      false,
+      context)
+  }
 }
 
 class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] {
   override def timerName(): String = Timers.WriteBAMRecord.timerName
   override def outputFormatClass(): Class[_ <: OutputFormat[K, SAMRecordWritable]] = classOf[ADAMBAMOutputFormatHeaderLess[K]]
-}
+}

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.scala

@@ -17,11 +17,18 @@
  */
 package org.bdgenomics.adam.rdd.read
 
-import org.seqdoop.hadoop_bam.{ SAMRecordWritable, KeyIgnoringAnySAMOutputFormat, SAMFormat }
 import htsjdk.samtools.SAMFileHeader
+import hbparquet.hadoop.util.ContextUtil
+import org.apache.hadoop.fs.Path
+import org.apache.hadoop.mapreduce.{ OutputFormat, RecordWriter, TaskAttemptContext }
 import org.apache.spark.rdd.InstrumentedOutputFormat
 import org.bdgenomics.adam.instrumentation.Timers
-import org.apache.hadoop.mapreduce.OutputFormat
+import org.seqdoop.hadoop_bam.{
+  KeyIgnoringAnySAMOutputFormat,
+  KeyIgnoringSAMRecordWriter,
+  SAMFormat,
+  SAMRecordWritable
+}
 
 object ADAMSAMOutputFormat extends Serializable {
 
@@ -76,9 +83,23 @@ class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, org
 class ADAMSAMOutputFormatHeaderLess[K]
     extends KeyIgnoringAnySAMOutputFormat[K](SAMFormat.valueOf("SAM")) with Serializable {
 
-  setSAMHeader(ADAMSAMOutputFormat.getHeader)
   setWriteHeader(false)
 
+  override def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable] = {
+    val conf = ContextUtil.getConfiguration(context)
+
+    // where is our header file?
+    val path = new Path(conf.get("org.bdgenomics.adam.rdd.read.bam_header_path"))
+
+    // read the header file
+    readSAMHeaderFrom(path, conf)
+
+    // now that we have the header set, we need to make a record reader
+    return new KeyIgnoringSAMRecordWriter(getDefaultWorkFile(context, ""),
+      header,
+      false,
+      context)
+  }
 }
 
 class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, org.seqdoop.hadoop_bam.SAMRecordWritable] {