From 6d148a5edb1edce065b0f23ee2c884a500a6ec83 Mon Sep 17 00:00:00 2001
From: Gisli Magnusson <gmagnusson@genedx.com>
Date: Mon, 26 Jan 2026 17:47:53 +0000
Subject: [PATCH] fix(ENGKNOW-3055):  Fix replace on no matching columns.

---
 .../gorsat/Analysis/ReplaceAnalysis.scala     | 26 ++++++++++---------
 .../main/scala/gorsat/Commands/Replace.scala  |  2 +-
 .../src/test/java/gorsat/UTestReplace.java    |  9 +++++++
 3 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/gortools/src/main/scala/gorsat/Analysis/ReplaceAnalysis.scala b/gortools/src/main/scala/gorsat/Analysis/ReplaceAnalysis.scala
index 2866f3a26..ea4259de4 100644
--- a/gortools/src/main/scala/gorsat/Analysis/ReplaceAnalysis.scala
+++ b/gortools/src/main/scala/gorsat/Analysis/ReplaceAnalysis.scala
@@ -72,18 +72,20 @@ case class ReplaceAnalysis(context: GorContext, executeNor: Boolean, paramString
   }
 
   override def process(r: Row): Unit = {
-    val cvp = ReplaceCvp(r)
-    try {
-       val columnValues = columnsToReplace.indices.map(i => {
-         cvp.replaceCol = columnsToReplace(i)
-         val exIx = if(i > expressions.length - 1) 0 else i
-         evalFunction(cvp, expressions(exIx), expressionTypes(exIx))
-       })
-      r.setColumns(columnsToReplace, columnValues.toArray)
-    } catch {
-      case e: GorParsingException =>
-        val msg = s"Error in step: REPLACE $paramString\n${e.getMessage}"
-        throw new GorDataException(msg, -1, header, r.getAllCols.toString, e)
+    if (!columnsToReplace.isEmpty) {
+      val cvp = ReplaceCvp(r)
+      try {
+        val columnValues = columnsToReplace.indices.map(i => {
+          cvp.replaceCol = columnsToReplace(i)
+          val exIx = if (i > expressions.length - 1) 0 else i
+          evalFunction(cvp, expressions(exIx), expressionTypes(exIx))
+        })
+        r.setColumns(columnsToReplace, columnValues.toArray)
+      } catch {
+        case e: GorParsingException =>
+          val msg = s"Error in step: REPLACE $paramString\n${e.getMessage}"
+          throw new GorDataException(msg, -1, header, r.getAllCols.toString, e)
+      }
     }
     super.process(r)
   }
diff --git a/gortools/src/main/scala/gorsat/Commands/Replace.scala b/gortools/src/main/scala/gorsat/Commands/Replace.scala
index 10c5f2871..aa14348b4 100644
--- a/gortools/src/main/scala/gorsat/Commands/Replace.scala
+++ b/gortools/src/main/scala/gorsat/Commands/Replace.scala
@@ -38,7 +38,7 @@ class Replace extends CommandInfo("REPLACE",
     val colNums = columnsFromHeader(colName, forcedInputHeader, executeNor).toArray
 
     val filteredColNums = colNums.filter(i => i>= 2)
-    if(filteredColNums.isEmpty) {
+    if(!colNums.isEmpty && filteredColNums.isEmpty) {
       throw new GorParsingException("REPLACE is not allowed on Chrom/Pos columns")
     }
     CommandParsingResult(ReplaceAnalysis(context, executeNor, formula, forcedInputHeader, filteredColNums), forcedInputHeader)
diff --git a/gortools/src/test/java/gorsat/UTestReplace.java b/gortools/src/test/java/gorsat/UTestReplace.java
index 1ae034f39..5b1a6265b 100644
--- a/gortools/src/test/java/gorsat/UTestReplace.java
+++ b/gortools/src/test/java/gorsat/UTestReplace.java
@@ -97,4 +97,13 @@ public void replaceStarWhenUsingNor() {
                 "chrN\t0\t42\t42\t42\t42\n";
         Assert.assertEquals(expected, res);
     }
+
+    @Test
+    public void replaceNoExistingColumns() {
+        String query = "gorrow chr1,1 " +
+                "| replace Foo_* if(#rc='0','wt',#rc)";
+        String result = TestUtils.runGorPipe(query);
+        Assert.assertEquals("chrom\tpos\nchr1\t1\n", result);
+    }
+
 }