Fixed bug for files with no newlines.

src/mergeFile/mergeMain.cpp

@@ -70,11 +70,9 @@ void merge_help(void) {
     cerr						<<  "\t\tMultiple columns can be specified in a comma-delimited list." << endl << endl;
 
     KeyListOpsHelp();
-        cerr << "Notes: " << endl;
-    cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
-    cerr << "\t    will in BED format with zero-based starts" << endl << endl;
-
-    cerr << "\t(2) The input file (-i) file must be sorted by chrom, then start." << endl << endl;
+    cerr << "Notes: " << endl;
+ 
+    cerr << "\t(1) The input file (-i) file must be sorted by chrom, then start." << endl << endl;
 
     // end the program here
     exit(1);

src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp

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

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp

@@ -28,7 +28,8 @@ InputStreamMgr::InputStreamMgr(const QuickString &filename, bool buildScanBuffer
  _streamFinished(false),
  _numBytesInBuffer(0),
  _bamReader(NULL),
- _bgStream(NULL)
+ _bgStream(NULL),
+ _eofHit(false)
 {
 	_possibleBamCode.resize(4, 0);
 }
@@ -138,6 +139,7 @@ bool InputStreamMgr::populateScanBuffer()
 		currChar = _pushBackStreamBuf->sbumpc();
 		//Stop when EOF hit.
 		if (currChar == EOF) {
+			_eofHit = true;
 			break;
 		}
 		numChars++;
@@ -185,6 +187,7 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
 				currChar = _pushBackStreamBuf->sbumpc();
 				//Stop when EOF hit.
 				if (currChar == EOF) {
+					_eofHit = true;
 					break;
 				}
 				_scanBuffer.push_back(currChar);

src/utils/FileRecordTools/FileReaders/InputStreamMgr.h

@@ -38,7 +38,7 @@ public:
 	bool isBam() const { return _isBam; }
 	BamTools::BamReader *getBamReader() { return _bamReader; }
 	bool resetStream();
-
+	bool getEofHit() { return _eofHit; }
 
 private:
 	QuickString _filename;
@@ -63,6 +63,7 @@ private:
 	int _numBytesInBuffer; //this will hold the length of the buffer after the scan.
 	BamTools::BamReader *_bamReader;
 	BamTools::Internal::BgzfStream *_bgStream;
+	bool _eofHit;
 
 	static const char *FIFO_STRING_LITERAL;
 	bool readZipChunk();

src/utils/fileType/FileRecordTypeChecker.cpp

@@ -4,6 +4,7 @@
 #include "ParseTools.h"
 
 FileRecordTypeChecker::FileRecordTypeChecker()
+: _eofHit(false)
 {
 	_fileType = UNKNOWN_FILE_TYPE;
 	_recordType = UNKNOWN_RECORD_TYPE;
@@ -71,11 +72,9 @@ FileRecordTypeChecker::FileRecordTypeChecker()
 }
 
 
-bool FileRecordTypeChecker::scanBuffer(const char *buffer, size_t len)
+bool FileRecordTypeChecker::scanBuffer(const char *buffer, size_t len, bool eofHit)
 {
-	if (len == 0) {
-		len = strlen(buffer);
-	}
+	_eofHit = eofHit;
 	_numBytesInBuffer = len;
 	if (_numBytesInBuffer == 0) {
 		_fileType = EMPTY_FILE_TYPE;
@@ -261,7 +260,7 @@ bool FileRecordTypeChecker::isTextDelimtedFormat(const char *buffer, size_t len)
 {
 	//Break single string buffer into vector of QuickStrings. Delimiter is newline.
 	_tokenizer.setKeepFinalIncompleteElem(Tokenizer::IGNORE);
-	int numLines = _tokenizer.tokenize(buffer, '\n');
+	int numLines = _tokenizer.tokenize(buffer, '\n', _eofHit);
 
 	//anticipated delimiter characters are tab, comma, and semi-colon.
 	//If we need new ones, they must be added in this method.

src/utils/fileType/FileRecordTypeChecker.h

@@ -34,7 +34,7 @@ public:
 		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 scanBuffer(const char *buf, size_t len, bool eofHit);
 	bool needsMoreData() const { return _insufficientData; }
 
 	bool recordTypeHasName(RECORD_TYPE type) const { return _hasName.find(type) != _hasName.end(); }
@@ -114,6 +114,8 @@ private:
 	map<RECORD_TYPE, bool> _hasScore;
 	map<RECORD_TYPE, bool> _hasStrand;
 
+	bool _eofHit;
+
 	//this will be used in determining whether we are looking at a binary or text file.
 	static const float PERCENTAGE_PRINTABLE = .9;
 	bool isBinaryBuffer(const char *buffer, size_t len);

src/utils/general/Tokenizer.cpp

@@ -27,7 +27,7 @@ void Tokenizer::setNumExpectedItems(int newSize) {
 	resize(newSize);
 }
 
-int Tokenizer::tokenize(const QuickString &str, char delimiter) {
+int Tokenizer::tokenize(const QuickString &str, char delimiter, bool eofHit) {
 
 	int strLen = (int)str.size();
 
@@ -41,7 +41,8 @@ int Tokenizer::tokenize(const QuickString &str, char delimiter) {
 			currPos++;
 		}
 		if (currPos > startPos) {
-			if (currPos == strLen && _keepFinalIncElem != USE_NOW) {
+			if ((currPos == strLen && _keepFinalIncElem != USE_NOW) &&
+					(!(delimiter == '\n' && eofHit))) {
 				//we found an incomplete final element.
 				// if we're ignoring incomplete elems, do nothing with it.
 				currIdx--; //make sure it's not included in the final count of valid elems.

src/utils/general/Tokenizer.h

@@ -22,7 +22,7 @@ public:
 	// If not, don't worry about it.
 	void setNumExpectedItems(int val);
 
-	int tokenize(const QuickString &str, char delimiter = '\t');
+	int tokenize(const QuickString &str, char delimiter = '\t', bool eofHit = false);
 
 	// If the final element ends before a delim char, that means
 	// the buffer passed in ends mid-element. The last, incomplete

test/intersect/new_test-intersect.sh

@@ -755,3 +755,12 @@ chr1	14750216	15119039" >exp
 check exp obs
 rm exp obs
 
+###########################################################
+#  Test that files with no newlines at all are handled
+############################################################
+echo "    intersect.new.t64...\c"
+echo "chr17	7577068	7577157" > exp
+$BT intersect -a oneRecordNoNewline.bed -b oneRecordNoNewline.bed > obs
+check obs exp
+rm obs exp
+

test/intersect/oneRecordNoNewline.bed

+chr17	7577068	7577157
\ No newline at end of file