From 91895424646b7afd805886006a7eda78a6cbd3f9 Mon Sep 17 00:00:00 2001
From: Gisli Magnusson <gmagnusson@genedx.com>
Date: Sun, 8 Feb 2026 00:50:09 +0000
Subject: [PATCH] fix(ENGKNOW-3014):  Fix norif context, and allow single
 column -dh for norif.

---
 .../gorsat/Utilities/gorsatUtilities.scala     | 18 +++++++++++++-----
 gortools/src/test/java/gorsat/UTestNorif.java  |  3 ++-
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/gortools/src/main/scala/gorsat/Utilities/gorsatUtilities.scala b/gortools/src/main/scala/gorsat/Utilities/gorsatUtilities.scala
index 404e68a8..ec557715 100644
--- a/gortools/src/main/scala/gorsat/Utilities/gorsatUtilities.scala
+++ b/gortools/src/main/scala/gorsat/Utilities/gorsatUtilities.scala
@@ -56,12 +56,20 @@ object Utilities {
       // return an iterator that only delivers the header defined with -dh.
       val header = stringValueOfOption(args, "-dh")
       val headerCols = header.split(",")
-      if (headerCols.length < 2 || headerCols(0).isEmpty || headerCols(1).isEmpty) {
-        throw new GorParsingException("-dh requires at least 2 non-empty comma-separated values")
-      }
       val inputSource = RowListIterator(List())
-      if (isNor) inputSource.setHeader(HEADER_PREFIX + headerCols.mkString("\t")) else inputSource.setHeader(headerCols.mkString("\t"))
-      InputSourceParsingResult(inputSource, header, isNorContext = false)
+      if (isNor) {
+        if (headerCols.length < 1 || headerCols(0).isEmpty) {
+          throw new GorParsingException("For NOR -dh requires at least 1 non-empty value")
+        }
+        inputSource.setHeader(HEADER_PREFIX + headerCols.mkString("\t"))
+      } else {
+        if (headerCols.length < 2 || headerCols(0).isEmpty || headerCols(1).isEmpty) {
+          throw new GorParsingException("For GOR -dh requires at least 2 non-empty comma-separated values")
+        }
+        inputSource.setHeader(headerCols.mkString("\t"))
+      }
+
+      InputSourceParsingResult(inputSource, header, isNorContext = isNor)
     }
   }
 
diff --git a/gortools/src/test/java/gorsat/UTestNorif.java b/gortools/src/test/java/gorsat/UTestNorif.java
index e08e2de6..b426fb4f 100644
--- a/gortools/src/test/java/gorsat/UTestNorif.java
+++ b/gortools/src/test/java/gorsat/UTestNorif.java
@@ -80,9 +80,10 @@ public static Collection<Object[]> data() throws IOException {
                 {"Nested query started with norif", "norif <(nor " + testTsvFile1 + ")",
                     expectedHeader + "chrN\t0\tA\t1\tA\n", null},
                 {"Invalid file path", "norif -dh col1,col2 not_exists.tsv", HEADER_PREFIX+ "col1\tcol2\n", null},
+                {"Invalid file path, single col", "norif -dh col1 not_exists.tsv", HEADER_PREFIX+ "col1\n", null},
                 {"Invalid file path missing -dh", "norif not_exists.tsv", null, GorParsingException.class},
                 {"Empty file missing -dh", "norif " + testEmptyFile, null, GorParsingException.class},
-                {"Invalid file path with invalid -dh value", "norif -dh col1 not_exists.tsv", null, GorParsingException.class},
+                {"Invalid file path with invalid -dh value", "norif not_exists.tsv -dh  ", null, GorParsingException.class},
                 {"Both invalid and valid file path", "norif " + testTsvFile1 + " not_exists.tsv",
                     expectedHeader + "chrN\t0\tA\t1\tA\n", null},
         });