hail-is · patrick-schultz · Jan 29, 2026
diff --git a/hail/hail/ir-gen/src/Main.scala b/hail/hail/ir-gen/src/Main.scala
@@ -76,8 +76,7 @@ trait IRDSL {
   val BaseRef: Trait
   def TypedIR(t: String): Trait
   val NDArrayIR: Trait
-  // AbstractApplyNodeUnseededMissingness{Aware, Oblivious}JVMFunction
-  def ApplyNode(missingnessAware: Boolean = false): Trait
+  val ApplyNode: Trait
 
   // Implicits for common names
 
@@ -121,12 +120,7 @@ object IRDSL_Impl extends IRDSL {
   override val BaseRef: Trait = Trait("BaseRef")
   override def TypedIR(typ: String): Trait = Trait(s"TypedIR[$typ]")
   override val NDArrayIR: Trait = Trait("NDArrayIR")
-
-  override def ApplyNode(missingnessAware: Boolean = false): Trait = {
-    val t =
-      s"AbstractApplyNode[UnseededMissingness${if (missingnessAware) "Aware" else "Oblivious"}JVMFunction]"
-    Trait(t)
-  }
+  override val ApplyNode: Trait = Trait("AbstractApplyNode")
 
   trait Repr[+T] {
     def typ: Type[T]
@@ -1109,7 +1103,7 @@ object Main {
       in("args", child.*),
       in("returnType", att("Type")),
       errorID,
-    ).withTraits(ApplyNode())
+    ).withTraits(ApplyNode)
 
     r += node(
       "ApplySeeded",
@@ -1118,19 +1112,10 @@ object Main {
       in("rngState", child),
       in("staticUID", att("Long")),
       in("returnType", att("Type")),
-    ).withTraits(ApplyNode())
+    ).withTraits(ApplyNode)
       .withPreamble("val args = rngState +: _args")
       .withPreamble("val typeArgs: Seq[Type] = Seq.empty[Type]")
 
-    r += node(
-      "ApplySpecial",
-      in("function", att("String")),
-      in("typeArgs", att("Seq[Type]")),
-      in("args", child.*),
-      in("returnType", att("Type")),
-      errorID,
-    ).withTraits(ApplyNode(missingnessAware = true))
-
     r += node("LiftMeOut", in("child", child))
 
     r += node("TableCount", tableChild)
@@ -1222,8 +1207,8 @@ object Main {
         "BlockMatrixMultiWriter, ValueReader, ValueWriter}",
       "is.hail.expr.ir.lowering.TableStageDependency",
       "is.hail.expr.ir.agg.{PhysicalAggSig, AggStateSig}",
-      "is.hail.expr.ir.functions.{UnseededMissingnessAwareJVMFunction, " +
-        "UnseededMissingnessObliviousJVMFunction, TableToValueFunction, MatrixToValueFunction, " +
+      "is.hail.expr.ir.functions.{MissingnessAwareJVMFunction, " +
+        "MissingnessObliviousJVMFunction, TableToValueFunction, MatrixToValueFunction, " +
         "BlockMatrixToValueFunction}",
       "is.hail.expr.ir.defs.exts._",
       "scala.collection.compat._",

diff --git a/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala
@@ -163,14 +163,7 @@ class BlockMatrixNativeReader(
     val reader = ETypeValueReader(spec)
 
     def blockIR(ctx: IR): IR = {
-      val path = Apply(
-        "concat",
-        FastSeq(),
-        FastSeq(Str(s"${params.path}/parts/"), ctx),
-        TString,
-        ErrorIDs.NO_ERROR,
-      )
-
+      val path = invoke("concat", TString, Str(s"${params.path}/parts/"), ctx)
       ReadValue(path, reader, vType)
     }
 

diff --git a/hail/hail/src/is/hail/expr/ir/Emit.scala b/hail/hail/src/is/hail/expr/ir/Emit.scala
@@ -9,6 +9,7 @@ import is.hail.expr.ir.analyses.{
 }
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs._
+import is.hail.expr.ir.functions.{MissingnessAwareJVMFunction, MissingnessObliviousJVMFunction}
 import is.hail.expr.ir.lowering.TableStageDependency
 import is.hail.expr.ir.ndarrays.EmitNDArray
 import is.hail.expr.ir.streams.{EmitStream, StreamProducer, StreamUtils}
@@ -2771,14 +2772,53 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
         val rvAgg = agg.Extract.getAgg(sig)
         rvAgg.result(cb, sc.states(idx), region)
 
+      case ir @ Apply(fn, typeArgs, args, rt, errorID) =>
+        ir.implementation match {
+          case impl: MissingnessObliviousJVMFunction =>
+            val unified = impl.unify(typeArgs, args.map(_.typ), rt)
+            assert(unified)
+
+            IEmitCode.multiMap(
+              cb,
+              args.map(arg => (cb: EmitCodeBuilder) => emitInNewBuilder(cb, arg)),
+            ) { codeArgs =>
+              val argSTypes = codeArgs.map(_.st)
+              val retType = impl.computeStrictReturnEmitType(ir.typ, argSTypes)
+              val k = (fn, typeArgs, argSTypes, retType)
+              val meth =
+                methods.get(k) match {
+                  case Some(funcMB) =>
+                    funcMB
+                  case None =>
+                    val funcMB = impl.getAsMethod(mb.ecb, retType, typeArgs, argSTypes: _*)
+                    methods.update(k, funcMB)
+                    funcMB
+                }
+              cb.invokeSCode(
+                meth,
+                FastSeq[Param](cb.this_, CodeParam(region), CodeParam(errorID)) ++ codeArgs.map(
+                  pc =>
+                    pc: Param
+                ): _*
+              )
+            }
+
+          case impl: MissingnessAwareJVMFunction =>
+            val codeArgs = args.map(a => EmitCode.fromI(cb.emb)(emitInNewBuilder(_, a)))
+            val unified = impl.unify(typeArgs, args.map(_.typ), rt)
+            assert(unified)
+            val retType = impl.computeReturnEmitType(ir.typ, codeArgs.map(_.emitType))
+            impl.apply(cb, region, retType.st, typeArgs, errorID, codeArgs: _*)
+        }
+
       case x @ ApplySeeded(_, args, rngState, staticUID, rt) =>
         val codeArgs = args.map(a => EmitCode.fromI(cb.emb)(emitInNewBuilder(_, a)))
         val codeArgsMem = codeArgs.map(_.memoize(cb, "ApplySeeded_arg"))
         val state = emitI(rngState).getOrAssert(cb)
         val impl = x.implementation
         assert(impl.unify(Array.empty[Type], x.argTypes, rt))
         val newState = EmitCode.present(mb, state.asRNGState.splitStatic(cb, staticUID))
-        impl.applyI(
+        impl.asInstanceOf[MissingnessObliviousJVMFunction].applyI(
           region,
           cb,
           impl.computeReturnEmitType(x.typ, newState.emitType +: codeArgs.map(_.emitType)).st,
@@ -3497,45 +3537,6 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
           )
         ev.load
 
-      case ir @ Apply(fn, typeArgs, args, rt, errorID) =>
-        val impl = ir.implementation
-        val unified = impl.unify(typeArgs, args.map(_.typ), rt)
-        assert(unified)
-
-        val emitArgs = args.map(a => EmitCode.fromI(mb)(emitI(a, _))).toFastSeq
-
-        val argSTypes = emitArgs.map(_.st)
-        val retType = impl.computeStrictReturnEmitType(ir.typ, argSTypes)
-        val k = (fn, typeArgs, argSTypes, retType)
-        val meth =
-          methods.get(k) match {
-            case Some(funcMB) =>
-              funcMB
-            case None =>
-              val funcMB = impl.getAsMethod(mb.ecb, retType, typeArgs, argSTypes: _*)
-              methods.update(k, funcMB)
-              funcMB
-          }
-        EmitCode.fromI(mb) { cb =>
-          val emitArgs = args.map(a => EmitCode.fromI(cb.emb)(emitI(a, _))).toFastSeq
-          IEmitCode.multiMapEmitCodes(cb, emitArgs) { codeArgs =>
-            cb.invokeSCode(
-              meth,
-              FastSeq[Param](cb.this_, CodeParam(region), CodeParam(errorID)) ++ codeArgs.map(pc =>
-                pc: Param
-              ): _*
-            )
-          }
-        }
-
-      case x @ ApplySpecial(_, typeArgs, args, rt, errorID) =>
-        val codeArgs = args.map(a => emit(a))
-        val impl = x.implementation
-        val unified = impl.unify(typeArgs, args.map(_.typ), rt)
-        assert(unified)
-        val retType = impl.computeReturnEmitType(x.typ, codeArgs.map(_.emitType))
-        impl.apply(mb, region, retType.st, typeArgs, errorID, codeArgs: _*)
-
       case WritePartition(stream, pctx, writer) =>
         val ctxCode = emit(pctx)
         val streamCode = emitStream(stream, region)

diff --git a/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala
@@ -809,12 +809,12 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
           },
           x.typ,
         )
-      case ApplySpecial("lor", _, _, _, _) => children match {
+      case Apply("lor", _, _, _, _) => children match {
           case Seq(ConstantValue(l: Boolean), ConstantValue(r: Boolean)) =>
             ConstantValue(l || r, TBoolean)
           case _ => AbstractLattice.top
         }
-      case ApplySpecial("land", _, _, _, _) => children match {
+      case Apply("land", _, _, _, _) => children match {
           case Seq(ConstantValue(l: Boolean), ConstantValue(r: Boolean)) =>
             ConstantValue(l && r, TBoolean)
           case _ => AbstractLattice.top
@@ -842,7 +842,7 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
         .restrict(keySet)
     case (IsNA(_), Seq(b: BoolValue)) => b.isNA.restrict(keySet)
     // collection contains
-    case (ApplySpecial("contains", _, _, _, _), Seq(ConstantValue(intervalVal), queryVal)) =>
+    case (Apply("contains", _, _, _, _), Seq(ConstantValue(intervalVal), queryVal)) =>
       (intervalVal: @unchecked) match {
         case null => BoolValue.allNA(keySet)
         case i: Interval => queryVal match {
@@ -891,9 +891,9 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
       }
     case (ApplyComparisonOp(op, _, _), Seq(l, r)) =>
       AbstractLattice.compare(l, r, op, keySet)
-    case (ApplySpecial("lor", _, _, _, _), Seq(l: BoolValue, r: BoolValue)) =>
+    case (Apply("lor", _, _, _, _), Seq(l: BoolValue, r: BoolValue)) =>
       BoolValue.or(l, r)
-    case (ApplySpecial("land", _, _, _, _), Seq(l: BoolValue, r: BoolValue)) =>
+    case (Apply("land", _, _, _, _), Seq(l: BoolValue, r: BoolValue)) =>
       BoolValue.and(l, r)
     case (ApplyUnaryPrimOp(Bang, _), Seq(x: BoolValue)) =>
       BoolValue.not(x)

diff --git a/hail/hail/src/is/hail/expr/ir/IR.scala b/hail/hail/src/is/hail/expr/ir/IR.scala
@@ -220,7 +220,7 @@ package defs {
       }
   }
 
-  trait AbstractApplyNode[F <: JVMFunction] extends IR {
+  trait AbstractApplyNode extends IR {
     def function: String
 
     def args: Seq[IR]
@@ -231,9 +231,10 @@ package defs {
 
     def argTypes: Seq[Type] = args.map(_.typ)
 
-    lazy val implementation: F =
+    lazy val implementation: JVMFunction =
       IRFunctionRegistry.lookupFunctionOrFail(function, returnType, typeArgs, argTypes)
-        .asInstanceOf[F]
+
+    def strictArgs: Boolean = implementation.isInstanceOf[MissingnessObliviousJVMFunction]
   }
 
   object PartitionReader {
@@ -779,15 +780,15 @@ package defs {
 
       def all(element: IR): IR =
         aggFoldIR(True()) { accum =>
-          ApplySpecial(
+          Apply(
             "land",
             Seq.empty[Type],
             FastSeq(accum, element),
             TBoolean,
             ErrorIDs.NO_ERROR,
           )
         } { (accum1, accum2) =>
-          ApplySpecial(
+          Apply(
             "land",
             Seq.empty[Type],
             FastSeq(accum1, accum2),

diff --git a/hail/hail/src/is/hail/expr/ir/InferType.scala b/hail/hail/src/is/hail/expr/ir/InferType.scala
@@ -79,7 +79,7 @@ object InferType {
           case _ => TBoolean
         }
       case a: ApplyIR => a.returnType
-      case a: AbstractApplyNode[_] =>
+      case a: AbstractApplyNode =>
         val typeArgs = a.typeArgs
         val argTypes = a.args.map(_.typ)
         assert(a.implementation.unify(typeArgs, argTypes, a.returnType))

diff --git a/hail/hail/src/is/hail/expr/ir/Interpret.scala b/hail/hail/src/is/hail/expr/ir/Interpret.scala
@@ -838,7 +838,7 @@ object Interpret extends Logging {
         interpret(result)
       case ir @ ApplyIR(_, _, _, _, _) =>
         interpret(ir.explicitNode, env, args)
-      case ApplySpecial("lor", _, Seq(left_, right_), _, _) =>
+      case Apply("lor", _, Seq(left_, right_), _, _) =>
         val left = interpret(left_)
         if (left == true)
           true
@@ -850,7 +850,7 @@ object Interpret extends Logging {
             null
           else false
         }
-      case ApplySpecial("land", _, Seq(left_, right_), _, _) =>
+      case Apply("land", _, Seq(left_, right_), _, _) =>
         val left = interpret(left_)
         if (left == false)
           false
@@ -862,7 +862,7 @@ object Interpret extends Logging {
             null
           else true
         }
-      case ir: AbstractApplyNode[_] =>
+      case ir: AbstractApplyNode =>
         val argTuple =
           PType.canonical(TTuple(ir.args.map(_.typ): _*)).setRequired(true).asInstanceOf[PTuple]
         ctx.r.pool.scopedRegion { region =>

diff --git a/hail/hail/src/is/hail/expr/ir/Parser.scala b/hail/hail/src/is/hail/expr/ir/Parser.scala
@@ -1384,8 +1384,6 @@ object IRParser {
         } yield ApplySeeded(function, args, rngState, staticUID, rt)
       case "ApplyIR" =>
         apply_like(ctx, ApplyIR.apply)(it)
-      case "ApplySpecial" =>
-        apply_like(ctx, ApplySpecial)(it)
       case "Apply" =>
         apply_like(ctx, Apply)(it)
       case "MatrixCount" =>

diff --git a/hail/hail/src/is/hail/expr/ir/Pretty.scala b/hail/hail/src/is/hail/expr/ir/Pretty.scala
@@ -429,8 +429,6 @@ class Pretty(
       FastSeq(s"$errorID", prettyIdentifier(function), prettyTypes(typeArgs), t.parsableString())
     case ApplySeeded(function, _, _, staticUID, t) =>
       FastSeq(prettyIdentifier(function), staticUID.toString, t.parsableString())
-    case ApplySpecial(function, typeArgs, _, t, errorID) =>
-      FastSeq(s"$errorID", prettyIdentifier(function), prettyTypes(typeArgs), t.parsableString())
     case SelectFields(_, fields) =>
       single(fillList(fields.view.map(f => text(prettyIdentifier(f)))))
     case LowerBoundOnOrderedCollection(_, _, onKey) => single(Pretty.prettyBooleanLiteral(onKey))

diff --git a/hail/hail/src/is/hail/expr/ir/Requiredness.scala b/hail/hail/src/is/hail/expr/ir/Requiredness.scala
@@ -822,7 +822,7 @@ class Requiredness(val usesAndDefs: UsesAndDefs, ctx: ExecuteContext) {
         requiredness.union(oldReq.required)
         requiredness.unionFrom(oldReq.field(idx))
       case x: ApplyIR => requiredness.unionFrom(lookup(x.body))
-      case x: AbstractApplyNode[_] => // FIXME: round-tripping via PTypes.
+      case x: AbstractApplyNode => // FIXME: round-tripping via PTypes.
         val argP = x.args.map { a =>
           val pt = lookup(a).canonicalPType(a.typ)
           EmitType(pt.sType, pt.required)

diff --git a/hail/hail/src/is/hail/expr/ir/Simplify.scala b/hail/hail/src/is/hail/expr/ir/Simplify.scala
@@ -63,14 +63,13 @@ object Simplify {
     */
   private[this] def hasMissingStrictChild(x: IR): Boolean = {
     x match {
-      case _: Apply |
-          _: ApplySeeded |
-          _: ApplyUnaryPrimOp |
+      case _: ApplyUnaryPrimOp |
           _: ApplyBinaryPrimOp |
           _: ArrayRef |
           _: ArrayLen |
           _: GetField |
           _: GetTupleElement => x.children.exists(_.isInstanceOf[NA])
+      case x: AbstractApplyNode if x.strictArgs => x.children.exists(_.isInstanceOf[NA])
       case ApplyComparisonOp(op, _, _) if op.strict => x.children.exists(_.isInstanceOf[NA])
       case _ => false
     }
@@ -933,7 +932,7 @@ object Simplify {
       case TableFilter(TableFilter(t, p1), p2) =>
         Some(TableFilter(
           t,
-          ApplySpecial("land", Array.empty[Type], Array(p1, p2), TBoolean, ErrorIDs.NO_ERROR),
+          Apply("land", Array.empty[Type], Array(p1, p2), TBoolean, ErrorIDs.NO_ERROR),
         ))
 
       case TableFilter(TableKeyBy(child, key, isSorted), p) =>
@@ -1400,22 +1399,22 @@ object Simplify {
         Some(
           MatrixFilterRows(
             child,
-            ApplySpecial("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
+            Apply("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
           )
         )
 
       case MatrixFilterCols(MatrixFilterCols(child, pred1), pred2) =>
         Some(
           MatrixFilterCols(
             child,
-            ApplySpecial("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
+            Apply("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
           )
         )
 
       case MatrixFilterEntries(MatrixFilterEntries(child, pred1), pred2) =>
         Some(MatrixFilterEntries(
           child,
-          ApplySpecial("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
+          Apply("land", FastSeq(), FastSeq(pred1, pred2), TBoolean, ErrorIDs.NO_ERROR),
         ))
 
       case MatrixMapGlobals(MatrixMapGlobals(child, ng1), ng2) =>

diff --git a/hail/hail/src/is/hail/expr/ir/TypeCheck.scala b/hail/hail/src/is/hail/expr/ir/TypeCheck.scala
@@ -543,7 +543,7 @@ object TypeCheck {
       case Trap(_) =>
       case ConsoleLog(msg, _) => assert(msg.typ == TString)
       case ApplyIR(_, _, _, _, _) =>
-      case x: AbstractApplyNode[_] =>
+      case x: AbstractApplyNode =>
         assert(x.implementation.unify(x.typeArgs, x.args.map(_.typ), x.returnType))
       case MatrixWrite(_, _) =>
       case MatrixMultiWrite(children, _) =>