[ADAM-783] Write @sq header lines in sorted order.

This change resolves #783. Specifically, now we write the SAM/BAM @sq header
lines using the same lexicographic ordering that we use for sorting records.

adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala

@@ -109,14 +109,22 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
    * @return Returns a SAM formatted sequence dictionary.
    */
   def toSAMSequenceDictionary: SAMSequenceDictionary = {
-    new SAMSequenceDictionary(records.map(_ toSAMSequenceRecord).toList)
+    import SequenceRecord._
+    new SAMSequenceDictionary(records.sorted.map(_ toSAMSequenceRecord).toList)
   }
 
   override def toString: String = {
     records.map(_.toString).fold("SequenceDictionary{")(_ + "\n" + _) + "}"
   }
 }
 
+object SequenceOrdering extends Ordering[SequenceRecord] {
+  def compare(a: SequenceRecord,
+              b: SequenceRecord): Int = {
+    a.name.compareTo(b.name)
+  }
+}
+
 /**
  * Utility class within the SequenceDictionary; represents unique reference name-to-id correspondence
  *
@@ -183,6 +191,8 @@ object SequenceRecord {
   val REFSEQ_TAG = "REFSEQ"
   val GENBANK_TAG = "GENBANK"
 
+  implicit def ordering = SequenceOrdering
+
   def apply(name: String,
             length: Long,
             md5: String = null,

adam-core/src/test/resources/sorted.sam

@@ -0,0 +1,10 @@
+@HD	VN:1.4	SO:unsorted
+@SQ	SN:1	LN:1000
+@SQ	SN:2	LN:1000
+@SQ     SN:3    LN:1000
+@SQ     SN:4    LN:2000
+A       0       1       1       50      10M     *       0       0       ACACACACAC      **********
+E       0       2       101     45      10M     *       0       0       ACACACACAC      **********
+D       0       2       501     55      10M2S   *       0       0       ACACACACACAC    ************
+B       0       3       11      40      4M2I4M  *       0       0       ACACACACAC      **********
+C       0       4       1001    25      8M      *       0       0       ACACACAC        ********

adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala

@@ -192,4 +192,20 @@ class SequenceDictionarySuite extends FunSuite {
     toSSD.assertSameDictionary(ssd)
   }
 
+  test("conversion to sam sequence dictionary has correct sort order") {
+    val sd = new SequenceDictionary(Vector(SequenceRecord("MT", 1000L),
+      SequenceRecord("4", 1000L),
+      SequenceRecord("1", 1000L),
+      SequenceRecord("3", 1000L),
+      SequenceRecord("2", 1000L),
+      SequenceRecord("X", 1000L)))
+    val ssd = sd.toSAMSequenceDictionary
+    val seq = ssd.getSequences
+    assert(seq.get(0).getSequenceName === "1")
+    assert(seq.get(1).getSequenceName === "2")
+    assert(seq.get(2).getSequenceName === "3")
+    assert(seq.get(3).getSequenceName === "4")
+    assert(seq.get(4).getSequenceName === "MT")
+    assert(seq.get(5).getSequenceName === "X")
+  }
 }

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctionsSuite.scala

@@ -24,6 +24,7 @@ import org.bdgenomics.adam.models._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.util.ADAMFunSuite
 import org.bdgenomics.formats.avro._
+import scala.io.Source
 import scala.util.Random
 
 class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
@@ -213,4 +214,89 @@ class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
         assert(readA.getReadName === readB.getReadName)
     }
   }
+
+  sparkTest("writing a small sorted file as SAM should produce the expected result") {
+    val reads = sc.parallelize(Seq(AlignmentRecord.newBuilder()
+      .setContig(Contig.newBuilder()
+        .setContigName("1")
+        .setContigLength(1000L)
+        .build())
+      .setStart(0L)
+      .setEnd(10L)
+      .setSequence("ACACACACAC")
+      .setQual("**********")
+      .setMapq(50)
+      .setCigar("10M")
+      .setReadName("A")
+      .build(),
+      AlignmentRecord.newBuilder()
+        .setContig(Contig.newBuilder()
+          .setContigName("3")
+          .setContigLength(1000L)
+          .build())
+        .setStart(10L)
+        .setEnd(20L)
+        .setSequence("ACACACACAC")
+        .setQual("**********")
+        .setMapq(40)
+        .setCigar("4M2I4M")
+        .setReadName("B")
+        .build(),
+      AlignmentRecord.newBuilder()
+        .setContig(Contig.newBuilder()
+          .setContigName("4")
+          .setContigLength(2000L)
+          .build())
+        .setStart(1000L)
+        .setEnd(1008L)
+        .setSequence("ACACACAC")
+        .setQual("********")
+        .setMapq(25)
+        .setCigar("8M")
+        .setReadName("C")
+        .build(),
+      AlignmentRecord.newBuilder()
+        .setContig(Contig.newBuilder()
+          .setContigName("2")
+          .setContigLength(1000L)
+          .build())
+        .setStart(500L)
+        .setEnd(510L)
+        .setSequence("ACACACACACAC")
+        .setQual("************")
+        .setMapq(55)
+        .setCigar("10M2S")
+        .setReadName("D")
+        .build(),
+      AlignmentRecord.newBuilder()
+        .setContig(Contig.newBuilder()
+          .setContigName("2")
+          .setContigLength(1000L)
+          .build())
+        .setStart(100L)
+        .setEnd(110L)
+        .setSequence("ACACACACAC")
+        .setQual("**********")
+        .setMapq(45)
+        .setCigar("10M")
+        .setReadName("E")
+        .build()), 1)
+
+    val tempFile = Files.createTempDirectory("sam")
+    val tempPath1 = tempFile.toAbsolutePath.toString + "/reads.sam"
+
+    reads.adamSortReadsByReferencePosition()
+      .adamSAMSave(tempPath1)
+
+    val file1 = Source.fromFile(tempPath1 + "/part-r-00000")
+    val file2 = Source.fromFile(ClassLoader.getSystemClassLoader
+      .getResource("sorted.sam").getFile)
+
+    val f1lines = file1.getLines
+    val f2lines = file2.getLines
+
+    assert(f1lines.size === f2lines.size)
+    f1lines.zip(f2lines)
+      .foreach(p => assert(p._1 === p._2))
+  }
 }