Merge 1e5450c into 4223f56

bigdatagenomics · Jan 16, 2018 · 5df7ca3 · 5df7ca3
2 parents 4223f56 + 1e5450c
commit 5df7ca3
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diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -1119,9 +1119,11 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     val files = getFsAndFilesWithFilter(pathName, new NoPrefixFileFilter("_"))
 
     // load yonder the metadata
-    files.map(p => loadSingleVcfMetadata(p.toString)).reduce((p1, p2) => {
+    val (sequences, samples, headerLines) = files.map(p => loadSingleVcfMetadata(p.toString)).reduce((p1, p2) => {
       (p1._1 ++ p2._1, p1._2 ++ p2._2, p1._3 ++ p2._3)
     })
+
+    (sequences, samples.distinct, headerLines)
   }
 
   /**

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
@@ -473,7 +473,13 @@ class ADAMContextSuite extends ADAMFunSuite {
   sparkTest("load vcf with a glob") {
     val path = testFile("bqsr1.vcf").replace("bqsr1", "*")
 
-    val variants = sc.loadVcf(path).toVariants
+    val vcs = sc.loadVcf(path)
+
+    assert(vcs.samples.size === 8)
+    assert(vcs.headerLines.size === 154)
+    assert(vcs.sequences.size === 31)
+
+    val variants = vcs.toVariants
     assert(variants.rdd.count === 782)
   }