From 1fc88967c7af93830ea15c54ef4dd5f6e164e641 Mon Sep 17 00:00:00 2001
From: Gisli Magnusson <gmagnusson@genedx.com>
Date: Wed, 18 Jun 2025 02:37:10 +0000
Subject: [PATCH] fix(ENGKNOW-2518):  Use long for line counts.

---
 gortools/src/main/java/gorsat/process/GorJavaUtilities.java | 2 +-
 .../scala/gorsat/QueryHandlers/GeneralQueryHandler.scala    | 4 ++--
 .../main/java/org/gorpipe/gor/binsearch/GorIndexFile.java   | 6 +++---
 model/src/main/java/org/gorpipe/gor/model/BaseMeta.java     | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/gortools/src/main/java/gorsat/process/GorJavaUtilities.java b/gortools/src/main/java/gorsat/process/GorJavaUtilities.java
index 0df4b7600..d56c3fe7b 100644
--- a/gortools/src/main/java/gorsat/process/GorJavaUtilities.java
+++ b/gortools/src/main/java/gorsat/process/GorJavaUtilities.java
@@ -591,7 +591,7 @@ public static void writeDictionaryFromMeta(FileReader fileReader, String outfold
             }
             var ai = new AtomicInteger();
             var entries = metaList.parallelStream()
-                .filter(meta -> !meta.containsProperty(GorMeta.HEADER_LINE_COUNT_KEY) || meta.getLineCount() > 0)
+                .filter(meta -> !meta.containsProperty(GorMeta.HEADER_LINE_COUNT_KEY) || meta.getLineCount() > 0L)
                 .map(meta -> {
                     var p = meta.getMetaPath();
                     // Assume we have all data in the root folder (note relatives does not work here for S3Shared).
diff --git a/gortools/src/main/scala/gorsat/QueryHandlers/GeneralQueryHandler.scala b/gortools/src/main/scala/gorsat/QueryHandlers/GeneralQueryHandler.scala
index 9d4d2a0c9..2141777bf 100644
--- a/gortools/src/main/scala/gorsat/QueryHandlers/GeneralQueryHandler.scala
+++ b/gortools/src/main/scala/gorsat/QueryHandlers/GeneralQueryHandler.scala
@@ -352,10 +352,10 @@ object GeneralQueryHandler {
         val metaPath = DataUtil.toFile(f, DataType.META)
         val opt: Optional[String] = if (fileReader.exists(metaPath)) {
           val meta = GorMeta.createAndLoad(fileReader, metaPath)
-          if (meta.getLineCount == -1) {
+          if (meta.getLineCount == -1L) {
             val ret = dictRangeFromSeekRange(x._2, prefix)
             Optional.of[String](ret)
-          } else if(meta.getLineCount > 0) {
+          } else if(meta.getLineCount > 0L) {
             Optional.of[String](prefix + meta.getRange().formatAsTabDelimited())
           } else {
             Optional.empty()
diff --git a/model/src/main/java/org/gorpipe/gor/binsearch/GorIndexFile.java b/model/src/main/java/org/gorpipe/gor/binsearch/GorIndexFile.java
index 4577b8bcd..54f0bbdcf 100644
--- a/model/src/main/java/org/gorpipe/gor/binsearch/GorIndexFile.java
+++ b/model/src/main/java/org/gorpipe/gor/binsearch/GorIndexFile.java
@@ -129,8 +129,8 @@ private void writeEntry(String chr, int pos, long filePos) throws IOException {
         }
     }
 
-    public static int loadVersion1(String line, BufferedReader reader, PositionCache pc) throws IOException {
-        int lineCount = 0;
+    public static long loadVersion1(String line, BufferedReader reader, PositionCache pc) throws IOException {
+        long lineCount = 0L;
         while (line != null) {
             String[] split = line.split("\t");
             StringIntKey key = new StringIntKey(split[0], Integer.parseInt(split[1]));
@@ -162,7 +162,7 @@ void invoke() throws IOException {
                     break;
                 case VERSION2:
                     // Version 1 and 2 have same format
-                    int lineCount = loadVersion1(line, reader, pc);
+                    long lineCount = loadVersion1(line, reader, pc);
                     log.debug("{} lines read from index file", lineCount);
                     break;
                 default:
diff --git a/model/src/main/java/org/gorpipe/gor/model/BaseMeta.java b/model/src/main/java/org/gorpipe/gor/model/BaseMeta.java
index b99251ce9..7bdc9fa95 100644
--- a/model/src/main/java/org/gorpipe/gor/model/BaseMeta.java
+++ b/model/src/main/java/org/gorpipe/gor/model/BaseMeta.java
@@ -173,11 +173,11 @@ public String getTags() {
         return getProperty(HEADER_TAGS_KEY);
     }
 
-    public int getLineCount() {
+    public long getLineCount() {
         if (headerProps.containsKey(HEADER_LINE_COUNT_KEY)) {
-            return Integer.parseInt(headerProps.get(HEADER_LINE_COUNT_KEY));
+            return Long.parseLong(headerProps.get(HEADER_LINE_COUNT_KEY));
         }
-        return -1;
+        return -1L;
     }
 
     public String[] getFileHeader() {