Index: core/include/seqan/store/store_io_gff.h
===================================================================
--- core/include/seqan/store/store_io_gff.h	(revision 13099)
+++ core/include/seqan/store/store_io_gff.h	(working copy)
@@ -223,11 +223,17 @@
 	// read fields of annotation line        
 	_parseSkipWhitespace(file, c);
 	
+    // check if empty line
+    if (c == '\n') {
+        _parseSkipLine(file,c);
+        return false;
+    }
+
 	// read column 1: contig name
 	// The letters until the first whitespace will be read.
 	// Then, we skip until we hit the first tab character.
 	_parseReadGffIdentifier(file, ctx.contigName, c);
-	if (!empty(ctx.contigName) && ctx.contigName[0] == '#')
+    if (!empty(ctx.contigName) && ctx.contigName[0] == '#')
 	{
 		_parseSkipLine(file, c);
 		return false;
@@ -255,7 +261,7 @@
 
 	// read column 5: end position
 	if (_parseIsDigit(c))
-		ctx.annotation.endPos = _parseReadNumber(file, c);
+        ctx.annotation.endPos = _parseReadNumber(file, c);
 	else 
 	{
 		ctx.annotation.endPos = TAnnotation::INVALID_POS;
@@ -453,7 +459,7 @@
 }
 
 template<typename TFile, typename TSpec, typename TConfig>
-inline void 
+inline bool
 read (
 	TFile & file,
 	FragmentStore<TSpec, TConfig> & fragStore,
@@ -462,7 +468,7 @@
 //IOREV _nodoc_
 	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
 	
-	if (_streamEOF(file)) return;
+    if (_streamEOF(file)) return false;
 
 	// get first character from the stream
 	char c = _streamGet(file);
@@ -480,17 +486,19 @@
 	_storeClearAnnoBackLinks(fragStore.annotationStore);
 	_storeCreateAnnoBackLinks(fragStore.annotationStore);
 	_storeRemoveTempAnnoNames(fragStore);
+
+    return true;
 }
 
 template<typename TFile, typename TSpec, typename TConfig>
-inline void 
+inline bool
 read (
 	TFile & file,
 	FragmentStore<TSpec, TConfig> & fragStore,
 	Gtf)
 {
 //IOREV _nodoc_ how do Gtf and Gff compare? nodoc for gtf
-	read (file, fragStore, Gff());
+    return read (file, fragStore, Gff());
 }
 
 //////////////////////////////////////////////////////////////////////////////