From 107ce14dcf51e3573baaa69e5063b22553c4a014 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Sun, 2 Jun 2019 14:29:44 -0500
Subject: [PATCH] add tests

---
 .../bdgenomics/adam/rdd/read/ReadDataset.scala   |  7 +++++--
 .../rdd/read/AlignmentRecordDatasetSuite.scala   | 13 +++++++++++++
 .../adam/rdd/read/ReadDatasetSuite.scala         | 16 ++++++++++++++++
 3 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala
index 2dbb9f0f05..2c39603a8a 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala
@@ -231,10 +231,13 @@ sealed abstract class ReadDataset extends AvroGenomicDataset[Read, ReadProduct,
       AlignmentRecord.newBuilder()
         .setReadName(read.getName)
         .setSequence(read.getSequence)
-        .setQuality(read.getQuality)
+        .setQuality(read.getQualityScores)
         .build()
     }
-    AlignmentRecordDataset(rdd.map(toAlignmentRecord), sequences)
+    AlignmentRecordDataset(rdd.map(toAlignmentRecord),
+      sequences,
+      ReadGroupDictionary.empty,
+      processingSteps = Seq.empty)
   }
 
   /**
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala
index 6accf636dc..9eb99488f5 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala
@@ -1860,4 +1860,17 @@ class AlignmentRecordDatasetSuite extends ADAMFunSuite {
 
     assert(reads.dataset.first().start.get === transformed.dataset.first().start.get)
   }
+
+  sparkTest("convert alignments to reads") {
+    val alignments = sc.loadAlignments(testFile("small.sam"))
+    val reads = alignments.toReads()
+    assert(alignments.sequences === reads.sequences)
+    assert(alignments.rdd.count === reads.rdd.count)
+
+    val first = reads.rdd.sortBy(_.getName).first()
+    assert(first.getName() === "simread:1:101556378:false")
+    assert(first.getSequence() === "TTTATTTTTTGAGCATGAAAGTAATATATGCTCAGTGTAAACAATTAGGTCATTATAAATATATTTAACAGGAAT")
+    assert(first.getLength() === 75L)
+    assert(first.getAlphabet() === org.bdgenomics.formats.avro.Alphabet.DNA)
+  }
 }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala
index c709ff70db..0799f7747f 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala
@@ -139,6 +139,22 @@ class ReadDatasetSuite extends ADAMFunSuite {
     assert(kv._2 === feature)
   }
 
+  sparkTest("convert reads to alignments") {
+    val reads: ReadDataset = ReadDataset(sc.parallelize(Seq(r1, r2)))
+    val alignments = reads.toAlignments.rdd.collect()
+    assert(alignments.length === 2)
+
+    val a1 = alignments(0)
+    assert(a1.getReadName === "name1")
+    assert(a1.getSequence === "actg")
+    assert(a1.getQuality === "9999")
+
+    val a2 = alignments(1)
+    assert(a2.getReadName === "name2")
+    assert(a2.getSequence === "actg")
+    assert(a2.getQuality === "9999")
+  }
+
   sparkTest("convert reads to sequences") {
     val reads: ReadDataset = ReadDataset(sc.parallelize(Seq(r1, r2)))
     val sequences = reads.toSequences.rdd.collect()