From 40a7fa329608b39b674f79402103c07b89d8baee Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 10 Oct 2026 13:44:23 +0000
Subject: [PATCH] fix(core): track actual LineReader read lengths

Co-authored-by: jrfaller <3370556+jrfaller@users.noreply.github.com>
---
 .../com/github/gumtreediff/io/LineReader.java | 10 ++++----
 .../gumtreediff/test/TestTreeIoUtils.java     | 23 +++++++++++++++++++
 2 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/core/src/main/java/com/github/gumtreediff/io/LineReader.java b/core/src/main/java/com/github/gumtreediff/io/LineReader.java
index 9348aa7a1..762396ee5 100644
--- a/core/src/main/java/com/github/gumtreediff/io/LineReader.java
+++ b/core/src/main/java/com/github/gumtreediff/io/LineReader.java
@@ -54,10 +54,12 @@ public LineReader(Reader parent) {
     @Override
     public int read(char[] cbuf, int off, int len) throws IOException {
         int r = reader.read(cbuf, off, len);
-        for (int i = 0; i < len; i++)
-            if (cbuf[off + i] == '\n')
-                lines.add(currentPos + i);
-        currentPos += len;
+        if (r > 0) {
+            for (int i = 0; i < r; i++)
+                if (cbuf[off + i] == '\n')
+                    lines.add(currentPos + i);
+            currentPos += r;
+        }
         return r;
     }
 
diff --git a/core/src/test/java/com/github/gumtreediff/test/TestTreeIoUtils.java b/core/src/test/java/com/github/gumtreediff/test/TestTreeIoUtils.java
index 5821c4ae1..12b44e481 100644
--- a/core/src/test/java/com/github/gumtreediff/test/TestTreeIoUtils.java
+++ b/core/src/test/java/com/github/gumtreediff/test/TestTreeIoUtils.java
@@ -90,6 +90,29 @@ public void testLineReader() throws IOException {
         assertArrayEquals(new int[] { 3, 2 }, lr.positionFor(9));
     }
 
+    @Test
+    public void testLineReaderWithPartialReads() throws IOException {
+        StringReader reader = new StringReader("foo\nbar\nbaz\n") {
+            @Override
+            public int read(char[] cbuf, int off, int len) throws IOException {
+                return super.read(cbuf, off, Math.min(len, 2));
+            }
+        };
+        LineReader lr = new LineReader(reader);
+        char[] buffer = new char[8];
+        StringBuilder contents = new StringBuilder();
+        int count;
+
+        while ((count = lr.read(buffer, 0, buffer.length)) != -1)
+            contents.append(buffer, 0, count);
+
+        assertEquals("foo\nbar\nbaz\n", contents.toString());
+        assertEquals(4, lr.positionFor(2, 1));
+        assertEquals(8, lr.positionFor(3, 1));
+        assertArrayEquals(new int[] { 2, 1 }, lr.positionFor(4));
+        assertArrayEquals(new int[] { 3, 1 }, lr.positionFor(8));
+    }
+
     @Test
     public void testPrintTextTree() throws Exception {
         TreeContext tc = getTreeContext();