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diff --git a/src/utils/BamTools/._Makefile.fyKutp b/src/utils/BamTools/._Makefile.fyKutp
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diff --git a/src/utils/BamTools/BGZF.cpp b/src/utils/BamTools/BGZF.cpp
index 4fb7878516a892317dfe395f5c3d7073da28c053..d0242d6c7aaab52f6febc80933a016a99fcff55b 100644
--- a/src/utils/BamTools/BGZF.cpp
+++ b/src/utils/BamTools/BGZF.cpp
@@ -53,16 +53,11 @@ void BgzfData::Close(void) {
     // flush the BGZF block
     if ( IsWriteOnly ) { FlushBlock(); }
 
-	// write an empty block (as EOF marker)                                                                                                   
-	int blockLength = DeflateBlock();
-	fwrite(CompressedBlock, 1, blockLength, Stream);
-
     // flush and close
     fflush(Stream);
     fclose(Stream);
 }
 
-
 // compresses the current block
 int BgzfData::DeflateBlock(void) {
 
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