Added unit test and changed error message for empty files.

src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp

@@ -70,6 +70,7 @@ bool BufferedStreamMgr::init()
 bool BufferedStreamMgr::getTypeData()
 {
 	_currScanBuffer = _inputStreamMgr->getSavedData();
+	_typeChecker.setFilename(_filename);
 	do {
 		if (!_typeChecker.scanBuffer(_currScanBuffer.c_str(), _currScanBuffer.size()) && !_typeChecker.needsMoreData()) {
 			return false;

src/utils/fileType/FileRecordTypeChecker.cpp

@@ -77,7 +77,7 @@ bool FileRecordTypeChecker::scanBuffer(const char *buffer, size_t len)
 	}
 	_numBytesInBuffer = len;
 	if (_numBytesInBuffer == 0) {
-		cerr << "Error: Type checker received empty buffer." << endl;
+		cerr << "Error: " << _filename << " is an empty file."<< endl;
 		exit(1);
 	}
 

src/utils/fileType/FileRecordTypeChecker.h

@@ -32,6 +32,7 @@ public:
 	typedef enum  { UNKNOWN_RECORD_TYPE, BED3_RECORD_TYPE, BED4_RECORD_TYPE, BEDGRAPH_RECORD_TYPE, BED5_RECORD_TYPE,
 		BED6_RECORD_TYPE, BED12_RECORD_TYPE, BED_PLUS_RECORD_TYPE, BAM_RECORD_TYPE, VCF_RECORD_TYPE, GFF_RECORD_TYPE} RECORD_TYPE;
 
+	void setFilename(const QuickString & filename) { _filename = filename; }
 	bool scanBuffer(const char *buf, size_t len=0);
 	bool needsMoreData() const { return _insufficientData; }
 
@@ -80,6 +81,7 @@ private:
 	FILE_TYPE _fileType;
 	RECORD_TYPE _recordType;
 
+	QuickString _filename; //useful for reporting errors with file.
 	vector<QuickString> _lines;
 	vector<QuickString> _currLineElems;
 	int _firstValidDataLineIdx;

test/intersect/new_test-intersect.sh

@@ -584,6 +584,18 @@ $BT intersect -a nonExistantFile.bed -b b.bed -sorted 2>&1 > /dev/null | cat - >
 check obs exp
 rm obs exp
 
+###########################################################
+#  Test that we throw an error for empty files
+############################################################
+echo "    intersect.new.t51...\c"
+echo "is an empty file." > exp
+touch dummy.txt
+$BT intersect -a dummy.txt -b b.bed 2>&1 > /dev/null | cut -f3-6 --delimiter=' ' > obs
+check obs exp
+rm obs exp dummy.txt
+
+
+