[ADAM-1512] Support VCFs with +Inf/-Inf float values.

Resolves bigdatagenomics#1512.
fnothaft · Oct 8, 2017 · a703f18 · a703f18
1 parent 45b9fe8
commit a703f18
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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
@@ -1226,7 +1226,15 @@ class VariantContextConverter(
   private def toFloat(obj: java.lang.Object): Float = {
     tryAndCatchStringCast(obj, o => {
       o.asInstanceOf[java.lang.Float]
-    }, o => o.toFloat)
+    }, o => {
+      if (o == "+Inf") {
+        Float.PositiveInfinity
+      } else if (o == "-Inf") {
+        Float.NegativeInfinity
+      } else {
+        o.toFloat
+      }
+    })
   }
 
   // don't shadow toString

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
@@ -1484,6 +1484,20 @@ class VariantContextConverterSuite extends ADAMFunSuite {
     assert(va.getAlleleFrequency > 0.09f && va.getAlleleFrequency < 0.11f)
   }
 
+  test("single allele frequency is +Inf going htsjdk->adam") {
+    val acList: java.util.List[String] = List("+Inf")
+    val va = buildVariantAnnotation(Map(("AF", acList)),
+      converter.formatAlleleFrequency)
+    assert(va.getAlleleFrequency == Float.PositiveInfinity)
+  }
+
+  test("single allele frequency is -Inf going htsjdk->adam") {
+    val acList: java.util.List[String] = List("-Inf")
+    val va = buildVariantAnnotation(Map(("AF", acList)),
+      converter.formatAlleleFrequency)
+    assert(va.getAlleleFrequency == Float.NegativeInfinity)
+  }
+
   test("multiple allele frequencies going htsjdk->adam") {
     val acList: java.util.List[java.lang.Float] = List(
       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)