Fix tests

bigdatagenomics · Jan 16, 2019 · efbbe95 · efbbe95
1 parent a973b28
commit efbbe95
Show file tree

Hide file tree

Showing 2 changed files with 50 additions and 1 deletion.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
@@ -1979,7 +1979,14 @@ class VariantContextConverter(
         formatNonRefGenotypeLikelihoods(g, convertedCore, nrIndices)
       })
 
-      val vcAnns = VariantCallingAnnotations.newBuilder(coreWithOptNonRefs.build.getVariantCallingAnnotations)
+      val vcAnns = if (coreWithOptNonRefs.hasVariantCallingAnnotations) {
+        VariantCallingAnnotations.newBuilder(coreWithOptNonRefs.getVariantCallingAnnotations)
+      } else if (coreWithOptNonRefs.hasVariantCallingAnnotationsBuilder) {
+        VariantCallingAnnotations.newBuilder(coreWithOptNonRefs.getVariantCallingAnnotationsBuilder)
+      } else {
+        VariantCallingAnnotations.newBuilder
+      }
+
 
       // bind the annotation conversion functions and fold
       val boundAnnotationFns: Iterable[VariantCallingAnnotations.Builder => VariantCallingAnnotations.Builder] = genotypeAnnotationFormatFns

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
@@ -2764,4 +2764,46 @@ class VariantContextConverterSuite extends ADAMFunSuite {
     assert(optHtsjdkVc.isDefined)
     assert(optHtsjdkVc.get.getEnd === 16157602)
   }
+
+  sparkTest("keep info for non-ref in biallelic case") {
+    val vcRdd = sc.loadVcf(testFile("gvcf_dir/gvcf_multiallelic.g.vcf"))
+    val vcRecords = vcRdd.rdd.collect
+    val vcc = new VariantContextConverter(vcRdd.headerLines, lenient, true)
+
+    val biallelic = vcRecords.filter(_.variant.variant.getStart == 16157602L).head
+    val biallelicOptHtsjdkVc = vcc.convert(biallelic)
+
+    assert(biallelicOptHtsjdkVc.isDefined)
+    val biallelicVc = biallelicOptHtsjdkVc.get
+    assert(biallelicVc.hasAttribute("MLEAC") &&
+      biallelicVc.getAttributeAsIntList("MLEAC", -1).sameElements(List(1, 0)),
+      biallelicVc)
+    assert(biallelicVc.hasAttribute("MLEAF") &&
+      biallelicVc.getAttributeAsDoubleList("MLEAF", -1).sameElements(List(0.500, 0.00)))
+
+    val biallelicGt = biallelicVc.getGenotype("NA12878i")
+    assert(biallelicGt.hasPL && biallelicGt.getPL.sameElements(List(41, 3, 0, 41, 3, 41)))
+  }
+
+  sparkTest("keep info for non-ref in multi-allelic case") {
+    val vcRdd = sc.loadVcf(testFile("gvcf_dir/gvcf_multiallelic.g.vcf"))
+    val vcRecords = vcRdd.rdd.collect
+    val vcc = new VariantContextConverter(vcRdd.headerLines, lenient, true)
+
+    val multiallelic = vcRecords.filter(_.variant.variant.getStart == 18030095L)
+      .filter(_.variant.variant.getAlternateAllele == "TA")
+      .head
+    val multiallelicOptHtsjdkVc = vcc.convert(multiallelic)
+
+    assert(multiallelicOptHtsjdkVc.isDefined)
+    val multiallelicVc = multiallelicOptHtsjdkVc.get
+    assert(multiallelicVc.hasAttribute("MLEAC") &&
+      multiallelicVc.getAttributeAsIntList("MLEAC", -1).sameElements(List(1, 0)))
+    assert(multiallelicVc.hasAttribute("MLEAF") &&
+      multiallelicVc.getAttributeAsDoubleList("MLEAF", -1).sameElements(List(0.500, 0.00)))
+
+    val multiallelicGt = multiallelicVc.getGenotype("NA12878i")
+    assert(multiallelicGt.hasAD && multiallelicGt.getAD.sameElements(List(13, 17, 0)))
+    assert(multiallelicGt.hasPL && multiallelicGt.getPL.sameElements(List(602, 86, 553, 467, 353, 659)))
+  }
 }