From 49c70e5b394d303b47bd894d430f78f08aefc268 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Wed, 26 Sep 2018 10:39:35 -0400
Subject: [PATCH] fixing bug in SeekableHttpStream.read (#1182)

* fixing bug in SeekableHttpStream.read

* a bug in SeekableHttpStream could cause clients to go into an infinite loop because read would return 0 when trying to read one byte past the end of the file
* fixes #1181
---
 .../seekablestream/SeekableHTTPStream.java         |  5 ++++-
 .../seekablestream/SeekableBufferedStreamTest.java | 14 ++++++++++++++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java b/src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
index 640a14d989..a846fe4512 100644
--- a/src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
+++ b/src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
@@ -100,9 +100,12 @@ public int read(byte[] buffer, int offset, int len) throws IOException {
         if (offset < 0 || len < 0 || (offset + len) > buffer.length) {
             throw new IndexOutOfBoundsException("Offset="+offset+",len="+len+",buflen="+buffer.length);
         }
-        if (len == 0 || position == contentLength) {
+        if (len == 0 ) {
             return 0;
         }
+        if (position == contentLength) {
+            return -1;
+        }
 
         HttpURLConnection connection = null;
         InputStream is = null;
diff --git a/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
index f6e0b69899..4e498828db 100644
--- a/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
@@ -69,6 +69,20 @@ public void testRandomRead() throws IOException {
         assertEquals(buffer1, buffer2);
     }
 
+    @Test
+    public void testReadExactlyOneByteAtEndOfFile() throws IOException {
+        try (final SeekableStream stream = new SeekableHTTPStream(new URL(BAM_URL_STRING))){
+            byte[] buff = new byte[1];
+            long length = stream.length();
+            stream.seek(length - 1);
+            Assert.assertFalse(stream.eof());
+            Assert.assertEquals(stream.read(buff), 1);
+            Assert.assertTrue(stream.eof());
+            Assert.assertEquals(stream.read(buff), -1);
+        }
+    }
+
+
     /**
      * Test an attempt to read past the end of the file.  The test file is 594,149 bytes in length.  The test
      * attempts to read a 1000 byte block starting at position 594000.  A correct result would return 149 bytes.