fix old squiggly lines

hail-is · Sep 19, 2024 · 4576acf · 4576acf
1 parent 39413f7
commit 4576acf
Showing 1 changed file with 7 additions and 8 deletions.
diff --git a/hail/src/main/scala/is/hail/backend/py4j/Py4JBackendExtensions.scala b/hail/src/main/scala/is/hail/backend/py4j/Py4JBackendExtensions.scala
@@ -13,7 +13,7 @@ import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.io.reference.{IndexedFastaSequenceFile, LiftOver}
 import is.hail.linalg.RowMatrix
 import is.hail.types.physical.PStruct
-import is.hail.types.virtual.{TArray, TInterval, TStruct}
+import is.hail.types.virtual.{TArray, TInterval}
 import is.hail.utils.{defaultJSONFormats, fatal, log, toRichIterable, HailException, Interval}
 import is.hail.variant.ReferenceGenome
 
@@ -151,7 +151,7 @@ trait Py4JBackendExtensions {
  val tir = TableLiteral(
  TableValue(
  ctx,
- signature.virtualType.asInstanceOf[TStruct],
+ signature.virtualType,
  key,
  df.rdd,
  Some(signature),
@@ -176,17 +176,16 @@ trait Py4JBackendExtensions {
  case json4s.JObject(values) => values.toMap
  }
 
- val paths =
- kvs("paths").asInstanceOf[json4s.JArray].arr.toArray.map { case json4s.JString(s) =>
- s
- }
+ val paths = kvs("paths").asInstanceOf[json4s.JArray].arr.toArray.map {
+ case json4s.JString(s) => s
+ }
 
  val intervalPointType = parseType(kvs("intervalPointType").asInstanceOf[json4s.JString].s)
  val intervalObjects =
  JSONAnnotationImpex.importAnnotation(kvs("intervals"), TArray(TInterval(intervalPointType)))
  .asInstanceOf[IndexedSeq[Interval]]
 
- val opts = NativeReaderOptions(intervalObjects, intervalPointType, filterIntervals = false)
+ val opts = NativeReaderOptions(intervalObjects, intervalPointType)
  val matrixReaders: IndexedSeq[MatrixIR] = paths.map { p =>
  log.info(s"creating MatrixRead node for $p")
  val mnr = MatrixNativeReader(ctx.fs, p, Some(opts))
@@ -207,7 +206,7 @@ trait Py4JBackendExtensions {
  references(name).addLiftover(references(destRGName), LiftOver(ctx.fs, chainFile))
  }
 
- def pyRemoveLiftover(name: String, destRGName: String) =
+ def pyRemoveLiftover(name: String, destRGName: String): Unit =
  references(name).removeLiftover(destRGName)
 
  private[this] def addReference(rg: ReferenceGenome): Unit = {