From 1c2c39e257625fd27a95e3ad911882e425a7e1eb Mon Sep 17 00:00:00 2001
From: Kim Yang <kimy@nvidia.com>
Date: Fri, 21 Aug 2026 15:59:46 +0800
Subject: [PATCH] Fix BGZF truncation at embedded EOF markers

---
 src/bgzf.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/bgzf.h b/src/bgzf.h
index 8ad92e62..eb6eb241 100644
--- a/src/bgzf.h
+++ b/src/bgzf.h
@@ -147,7 +147,9 @@ class BgzfMtReader {
 
             if (bsize == 28) {
                 uint32_t isize = s.comp[24]|(s.comp[25]<<8)|(s.comp[26]<<16)|(s.comp[27]<<24);
-                if (isize == 0) { markDone(s); break; }
+                // An embedded BGZF EOF marker is just an empty block. It can
+                // appear when valid BGZF files are concatenated.
+                if (isize == 0) continue;
             }
 
             s.compLen = bsize;