Multiple DB intersect support with unit tests and updated help messages.

src/intersectFile/intersectMain.cpp

@@ -13,6 +13,7 @@ using namespace std;
 
 #include "intersectFile.h"
 #include "ContextIntersect.h"
+#include "CommonHelp.h"
 
 // define our program name
 #define PROGRAM_NAME "bedtools intersect"
@@ -46,6 +47,9 @@ void intersect_help(void) {
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
 
+    cerr << "\t\t"				<< "Note: -b may be followed with multiple databases and/or " << endl;
+    cerr << "\t\t"					"wildcard (*) character(s). " << endl;
+
     cerr << "Options: " << endl;
 
     cerr << "\t-abam\t"         << "The A input file is in BAM format.  Output will be BAM as well." << endl << endl;
@@ -119,6 +123,17 @@ void intersect_help(void) {
     cerr 						<<"\t\tother software tools and scripts that need to process one" << endl;
     cerr 						<<"\t\tline of bedtools output at a time." << endl << endl;
 
+    cerr << "\t-names\t"       << "When using multiple databases, provide an alias for each that" << endl;
+    cerr						<<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
+
+    cerr << "\t-filenames"       << "\tWhen using multiple databases, show each complete filename" << endl;
+    cerr						<<"\t\t\tinstead of a fileId when also printing the DB record." << endl << endl;
+
+    cerr << "\t-sortout\t"       << "When using multiple databases, sort the output DB hits" << endl;
+    cerr						<< "\t\t\tfor each record." << endl << endl;
+
+    CommonHelp();
+
     cerr << "Notes: " << endl;
     cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
     cerr << "\tand exlcuded if an overlap cannot be found.  If multiple overlaps exist, they are not" << endl;

src/utils/BinTree/BinTree.cpp

@@ -3,8 +3,7 @@
 
 
 BinTree::BinTree(ContextIntersect *context)
-: _databaseFile(NULL),
-  _context(context),
+:  _context(context),
   _binOffsetsExtended(NULL),
   _showBinMetrics(false),
   _maxBinNumFound(0)
@@ -36,7 +35,7 @@ BinTree::~BinTree() {
 				}
 				for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
 					const Record *record = listIter->value();
-					_databaseFile->deleteRecord(record);
+					_context->getFile(record->getFileIdx())->deleteRecord(record);
 				}
 				delete bin;
 				bin = NULL;
@@ -70,20 +69,22 @@ BinTree::~BinTree() {
 
 void BinTree::loadDB()
 {
-	_databaseFile = _context->getFile(_context->getDatabaseFileIdx());
-
-	Record *record = NULL;
-	while (!_databaseFile->eof()) {
-		record = _databaseFile->getNextRecord();
-		//In addition to NULL records, we also don't want to add unmapped reads.
-		if (record == NULL || record->isUnmapped()) {
-			continue;
-		}
+	for (int i=0; i < _context->getNumDatabaseFiles(); i++) {
+		FileRecordMgr *databaseFile = _context->getDatabaseFile(i);
+
+		Record *record = NULL;
+		while (!databaseFile->eof()) {
+			record = databaseFile->getNextRecord();
+			//In addition to NULL records, we also don't want to add unmapped reads.
+			if (record == NULL || record->isUnmapped()) {
+				continue;
+			}
 
-		if (!addRecordToTree(record)) {
-			fprintf(stderr, "ERROR: Unable to add record to tree.\n");
-			_databaseFile->close();
-			exit(1);
+			if (!addRecordToTree(record)) {
+				fprintf(stderr, "ERROR: Unable to add record to tree.\n");
+				databaseFile->close();
+				exit(1);
+			}
 		}
 	}
 }
@@ -149,6 +150,9 @@ void BinTree::getHits(Record *record, RecordKeyList &hitSet)
         startBin >>= _binNextShift;
         endBin >>= _binNextShift;
     }
+	if (_context->getSortOutput()) {
+		hitSet.sort();
+	}
 }
 
 bool BinTree::addRecordToTree(const Record *record)

src/utils/BinTree/BinTree.h

@@ -32,7 +32,6 @@ public:
 
 private:
 
-	FileRecordMgr *_databaseFile;
 	ContextIntersect *_context;
 
     //
@@ -52,8 +51,8 @@ private:
 	static const uint32_t _binFirstShift = 14;       /* How much to shift to get to finest bin. */
 	static const uint32_t _binNextShift  = 3;        /* How much to shift to get to next larger bin. */
 
-	typedef BTlist<const Record *> innerListType;
-	typedef const BTlistNode<const Record *> * innerListIterType;
+	typedef RecordList innerListType;
+	typedef const RecordListNode * innerListIterType;
 	typedef innerListType * binType;
 	typedef binType * allBinsType;
 	typedef QuickString mainKeyType;

src/utils/Contexts/ContextBase.cpp

@@ -36,18 +36,17 @@ ContextBase::ContextBase()
   _reciprocal(false),
   _sameStrand(false),
   _diffStrand(false),
-   _sortedInput(false),
+  _sortedInput(false),
+  _sortOutput(false),
+  _reportDBnameTags(false),
+  _reportDBfileNames(false),
   _printHeader(false),
   _printable(true),
    _explicitBedOutput(false),
   _queryFileIdx(-1),
-  _databaseFileIdx(-1),
   _bamHeaderAndRefIdx(-1),
   _maxNumDatabaseFields(0),
   _useFullBamTags(false),
-  _reportCount(false),
-  _reportNames(false),
-  _reportScores(false),
   _numOutputRecords(0),
   _hasConstantSeed(false),
   _seed(0),
@@ -193,6 +192,9 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-delim") == 0) {
 			if (!handle_delim()) return false;
         }
+        else if (strcmp(_argv[_i], "-sortout") == 0) {
+			if (!handle_sortout()) return false;
+        }
 
 	}
 	return true;
@@ -210,7 +212,11 @@ bool ContextBase::isValidState()
 		return false;
 	}
 	if (hasColumnOpsMethods()) {
-		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+
+		//TBD: Adjust column ops for multiple databases.
+		//For now, use last file.
+//		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+		FileRecordMgr *dbFile = getFile(getNumInputFiles()-1);
 		_keyListOps->setDBfileType(dbFile->getFileType());
 		if (!_keyListOps->isValidColumnOps(dbFile)) {
 			return false;
@@ -251,7 +257,7 @@ bool ContextBase::openFiles() {
 	_files.resize(_fileNames.size());
 
 	for (int i = 0; i < (int)_fileNames.size(); i++) {
-		FileRecordMgr *frm = getNewFRM(_fileNames[i]);
+		FileRecordMgr *frm = getNewFRM(_fileNames[i], i);
 		if (hasGenomeFile()) {
 			frm->setGenomeFile(_genomeFile);
 		}
@@ -281,7 +287,7 @@ int ContextBase::getBamHeaderAndRefIdx() {
 		if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
 			_bamHeaderAndRefIdx = _queryFileIdx;
 		} else {
-			_bamHeaderAndRefIdx = _databaseFileIdx;
+			_bamHeaderAndRefIdx = _dbFileIdxs[0];
 		}
 		return _bamHeaderAndRefIdx;
 	}
@@ -492,6 +498,13 @@ bool ContextBase::handle_delim()
     return true;
 }
 
+bool ContextBase::handle_sortout()
+{
+	setSortOutput(true);
+	markUsed(_i - _skipFirstArgs);
+	return true;
+}
+
 void ContextBase::setColumnOpsMethods(bool val)
 {
 	if (val && !_hasColumnOpsMethods) {
@@ -508,13 +521,17 @@ const QuickString &ContextBase::getColumnOpsVal(RecordKeyList &keyList) const {
 	return _keyListOps->getOpVals(keyList);
 }
 
-FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename) {
-	if (!_useMergedIntervals) {
-		return new FileRecordMgr(filename);
-	} else {
+FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename, int fileIdx) {
+
+	if (_useMergedIntervals) {
 		FileRecordMergeMgr *frm = new FileRecordMergeMgr(filename);
 		frm->setStrandType(_desiredStrand);
 		frm->setMaxDistance(_maxDistance);
+		frm->setFileIdx(fileIdx);
+		return frm;
+	} else {
+		FileRecordMgr *frm = new FileRecordMgr(filename);
+		frm->setFileIdx(fileIdx);
 		return frm;
 	}
 }

src/utils/Contexts/ContextBase.h

@@ -98,6 +98,15 @@ public:
     virtual bool getSortedInput() const {return _sortedInput; }
     virtual void setSortedInput(bool val) { _sortedInput = val; }
 
+    virtual bool getSortOutput() const {return _sortOutput; }
+    virtual void setSortOutput(bool val) { _sortOutput = val; }
+
+    virtual bool getUseDBnameTags() const { return _reportDBnameTags; }
+    virtual void setUseDBnameTags(bool val) { _reportDBnameTags = val; }
+
+    virtual bool getUseDBfileNames() const { return _reportDBfileNames; }
+    virtual void setUseDBfileNames(bool val) { _reportDBfileNames = val; }
+
     virtual bool getPrintHeader() const {return _printHeader; }
     virtual void setPrintHeader(bool val) { _printHeader = val; }
 
@@ -107,24 +116,6 @@ public:
     virtual bool getUseFullBamTags() const { return _useFullBamTags; }
     virtual void setUseFullBamTags(bool val) { _useFullBamTags = val; }
 
-//	//
-//	// MERGE METHODS
-//	//
-//    virtual bool getReportCount() const { return _reportCount; }
-//    virtual void setReportCount(bool val) { _reportCount = val; }
-//
-//    virtual int getMaxDistance() const { return _maxDistance; }
-//    virtual void setMaxDistance(int distance) { _maxDistance = distance; }
-//
-//    virtual bool getReportNames() const { return _reportNames; }
-//    virtual void setReportNames(bool val) { _reportNames = val; }
-//
-//    virtual bool getReportScores() const { return _reportScores; }
-//    virtual void setReportScores(bool val) { _reportScores = val; }
-//
-//    virtual const QuickString &getScoreOp() const { return _scoreOp; }
-//    virtual void setScoreOp(const QuickString &op) { _scoreOp = op; }
-
 
 	// METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER
 	// OF OUTPUT RECORDS.
@@ -192,18 +183,19 @@ protected:
     bool _sameStrand;
     bool _diffStrand;
     bool _sortedInput;
+    bool _sortOutput;
+    bool _reportDBnameTags;
+    bool _reportDBfileNames;
     bool _printHeader;
     bool _printable;
     bool _explicitBedOutput;
     int _queryFileIdx;
-    int _databaseFileIdx;
+    vector<int> _dbFileIdxs;
+    vector<QuickString> _dbNameTags;
+    map<int, int> _fileIdsToDbIdxs;
     int _bamHeaderAndRefIdx;
     int _maxNumDatabaseFields;
     bool _useFullBamTags;
-	bool _reportCount;
-	bool _reportNames;
-	bool _reportScores;
-	QuickString _scoreOp;
 
 	int _numOutputRecords;
 
@@ -227,7 +219,7 @@ protected:
 	bool isUsed(int i) const { return _argsProcessed[i]; }
 	bool cmdArgsValid();
 	bool openFiles();
-	virtual FileRecordMgr *getNewFRM(const QuickString &filename);
+	virtual FileRecordMgr *getNewFRM(const QuickString &filename, int fileIdx);
 
 	//set cmd line params and counter, i, as members so code
 	//is more readable (as opposed to passing all 3 everywhere).
@@ -256,6 +248,7 @@ protected:
 	virtual bool handle_o();
 	virtual bool handle_null();
 	virtual bool handle_delim();
+	virtual bool handle_sortout();
 
 	bool parseIoBufSize(QuickString bufStr);
 

src/utils/Contexts/ContextIntersect.cpp

@@ -44,6 +44,12 @@ bool ContextIntersect::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-b") == 0) {
 			if (!handle_b()) return false;
 		}
+        else if (strcmp(_argv[_i], "-names") == 0) {
+			if (!handle_names()) return false;
+		}
+        else if (strcmp(_argv[_i], "-filenames") == 0) {
+			if (!handle_filenames()) return false;
+		}
         else if (strcmp(_argv[_i], "-u") == 0) {
 			if (!handle_u()) return false;
         }
@@ -92,7 +98,7 @@ bool ContextIntersect::isValidState()
 		return false;
 	}
 
-	if (_queryFileIdx == -1 || _databaseFileIdx == -1) {
+	if (_queryFileIdx == -1 || _dbFileIdxs.size() == -0) {
 		_errorMsg = "\n***** ERROR: query and database files not specified. *****";
 		return false;
 	}
@@ -113,6 +119,11 @@ bool ContextIntersect::isValidState()
 			return false;
 		}
 	}
+	if (getUseDBnameTags() && _dbNameTags.size() != _dbFileIdxs.size()) {
+		_errorMsg = "\n***** ERROR: Number of database name tags given does not match number of databases. *****";
+		return false;
+
+	}
 	if (getWriteOverlap()) {
 
 		if (getWriteA()) {
@@ -149,7 +160,7 @@ bool ContextIntersect::isValidState()
 	if (getAnyHit() || getNoHit() || getWriteCount()) {
 		setPrintable(false);
 	}
-	if (_files.size() != 2 ) {
+	if (_files.size()  < 2 ) {
 		return false;
 	}
 	return true;
@@ -161,8 +172,8 @@ bool ContextIntersect::determineOutputType() {
 	}
 
 	//determine the maximum number of database fields.
-	for (int i=0; i < (int)_files.size(); i++) {
-		int numFields = _files[i]->getNumFields();
+	for (int i=0; i < getNumDatabaseFiles(); i++) {
+		int numFields = getDatabaseFile(i)->getNumFields();
 		if ( numFields > _maxNumDatabaseFields) {
 			_maxNumDatabaseFields = numFields;
 		}
@@ -211,19 +222,46 @@ bool ContextIntersect::handle_abam()
 bool ContextIntersect::handle_b()
 {
 	if (_argc <= _i+1) {
-		_errorMsg = "\n***** ERROR: -b option given, but no query file specified. *****";
+		_errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
 		return false;
 	}
 
-	addInputFile(_argv[_i+1]);
-	_databaseFileIdx = getNumInputFiles() -1;
-	markUsed(_i - _skipFirstArgs);
-	_i++;
-	markUsed(_i - _skipFirstArgs);
+	do {
+		addInputFile(_argv[_i+1]);
+		int fileId = getNumInputFiles() -1;
+		_dbFileIdxs.push_back(fileId);
+		_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
+		markUsed(_i - _skipFirstArgs);
+		_i++;
+		markUsed(_i - _skipFirstArgs);
+	} while (_argc > _i+1 && _argv[_i+1][0] != '-');
 	return true;
 }
 
 
+bool ContextIntersect::handle_names()
+{
+	if (_argc <= _i+1) {
+		_errorMsg = "\n***** ERROR: -b option given, but no database names specified. *****";
+		return false;
+	}
+
+	do {
+		addDatabaseNameTag(_argv[_i+1]);
+		markUsed(_i - _skipFirstArgs);
+		_i++;
+		markUsed(_i - _skipFirstArgs);
+	} while (_argc > _i+1 && _argv[_i+1][0] != '-');
+	setUseDBnameTags(true);
+	return true;
+}
+
+bool ContextIntersect::handle_filenames()
+{
+	markUsed(_i - _skipFirstArgs);
+	setUseDBfileNames(true);
+	return true;
+}
 
 bool ContextIntersect::handle_c()
 {

src/utils/Contexts/ContextIntersect.h

@@ -22,19 +22,22 @@ public:
 	//NOTE: Query and database files will only be marked as such by either the
 	//parseCmdArgs method, or by explicitly setting them.
 	FileRecordMgr *getQueryFile() { return getFile(_queryFileIdx); }
-	FileRecordMgr *getDatabaseFile() { return getFile(_databaseFileIdx); }
+	FileRecordMgr *getDatabaseFile(int idx) { return getFile(_dbFileIdxs[idx]); }
     int getQueryFileIdx() const { return _queryFileIdx; }
 	void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
-	int getDatabaseFileIdx() const { return _databaseFileIdx; }
-	void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
+	int getNumDatabaseFiles() { return (int)_dbFileIdxs.size(); }
+	const vector<int> &getDbFileIdxs() const { return _dbFileIdxs; }
 	const QuickString &getQueryFileName() const { return _files[_queryFileIdx]->getFileName(); }
-	const QuickString &getDatabaseFileName() const { return _files[_databaseFileIdx]->getFileName(); }
+	const QuickString &getDatabaseFileName(int idx) const { return _files[_dbFileIdxs[idx]]->getFileName(); }
 	ContextFileType getQueryFileType() const { return _files[_queryFileIdx]->getFileType(); }
-	ContextFileType getDatabaseFileType() const { return _files[_databaseFileIdx]->getFileType(); }
+	ContextFileType getDatabaseFileType(int idx) const { return _files[_dbFileIdxs[idx]]->getFileType(); }
 	ContextRecordType getQueryRecordType() const { return _files[_queryFileIdx]->getRecordType(); }
-	ContextRecordType getDatabaseRecordType() const { return _files[_databaseFileIdx]->getRecordType(); }
+	ContextRecordType getDatabaseRecordType(int idx) const { return _files[_dbFileIdxs[idx]]->getRecordType(); }
 	int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
 	void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
+	int getDbIdx(int fileId) { return _fileIdsToDbIdxs.find(fileId)->second; }
+	void addDatabaseNameTag(const QuickString &tag) { _dbNameTags.push_back(tag); }
+	const QuickString &getDatabaseNameTag(int dbIdx) const { return _dbNameTags[dbIdx]; }
 
 	bool getAnyHit() const {return _anyHit; }
 	void setAnyHit(bool val) { _anyHit = val; }
@@ -83,6 +86,9 @@ private:
 	virtual bool handle_a();
 	virtual bool handle_abam();
 	virtual bool handle_b();
+	virtual bool handle_names();
+	virtual bool handle_filenames();
+
 	virtual bool handle_c();
 	virtual bool handle_f();
 	virtual bool handle_loj();

src/utils/Contexts/ContextMap.cpp

@@ -47,3 +47,17 @@ bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
 	}
 	return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
 }
+
+bool ContextMap::isValidState()
+{
+	if (!ContextIntersect::isValidState()) {
+		return false;
+	}
+
+	// Multiple databases are currently not supported
+	if (getNumDatabaseFiles() > 1) {
+		_errorMsg = "\n***** ERROR: multiple database files currently not supported for map. *****";
+		return false;
+	}
+	return true;
+}

src/utils/Contexts/ContextMap.h

@@ -16,6 +16,8 @@ public:
 	virtual ~ContextMap();
 	virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
     virtual bool hasIntersectMethods() const { return true; }
+    virtual bool isValidState();
+
 
 private:
 

src/utils/FileRecordTools/FileReaders/FileReader.cpp

@@ -4,7 +4,7 @@
 #include "BufferedStreamMgr.h"
 
 FileReader::FileReader()
-:
+: _fileIdx(-1),
   _bufStreamMgr(NULL),
   _isFileOpen(false),
   _currChromId(-1)

src/utils/FileRecordTools/FileReaders/FileReader.h

@@ -16,6 +16,9 @@ public:
 	FileReader();
 	virtual ~FileReader();
 	void setFileName(const string &filename) { _filename = filename; }
+	virtual int getFileIdx() const { return _fileIdx; }
+	virtual void setFileIdx(int fileIdx) { _fileIdx = fileIdx; }
+
 	void setInputStream(BufferedStreamMgr *bufStreamMgr) {
 		_bufStreamMgr = bufStreamMgr;
 		_isFileOpen = true;
@@ -31,6 +34,7 @@ public:
 	virtual const QuickString &getHeader() const =0;
 	virtual int getNumFields() const = 0;
 protected:
+	int _fileIdx;
 	string _filename;
 	BufferedStreamMgr *_bufStreamMgr;
 

src/utils/FileRecordTools/FileRecordMgr.cpp

@@ -5,7 +5,7 @@
 #include "NewGenomeFile.h"
 
 FileRecordMgr::FileRecordMgr(const QuickString &filename)
-:
+: _fileIdx(-1),
   _filename(filename),
   _bufStreamMgr(NULL),
   _fileReader(NULL),
@@ -224,6 +224,7 @@ void FileRecordMgr::allocateFileReader()
 	default:
 		break;
 	}
+	_fileReader->setFileIdx(_fileIdx);
 }
 
 const BamTools::RefVector & FileRecordMgr::getBamReferences() {

src/utils/FileRecordTools/FileRecordMgr.h

@@ -37,6 +37,9 @@ public:
 	bool open();
 	void close();
 	virtual bool eof();
+	void setFileIdx(int fileIdx) { _fileIdx = fileIdx; }
+	int getFileIdx() const { return _fileIdx; }
+
 
 	//This is an all-in-one method to give the user a new record that is initialized with
 	//the next entry in the data file.
@@ -46,6 +49,7 @@ public:
 	void deleteRecord(const Record *);
 	virtual void deleteRecord(RecordKeyList *keyList);
 
+
 	const QuickString &getFileName() const { return _filename;}
 	bool hasHeader() const { return _fileReader->hasHeader(); }
 	const QuickString &getHeader() const { return _fileReader->getHeader(); }
@@ -103,6 +107,7 @@ public:
 	void setIoBufSize(int val) { _ioBufSize = val; }
 
 protected:
+	int _fileIdx;
 	QuickString _filename;
 	BufferedStreamMgr *_bufStreamMgr;
 

src/utils/FileRecordTools/Records/BamRecord.cpp

@@ -45,6 +45,7 @@ bool BamRecord::initFromFile(FileReader *fileReader)
 
 bool BamRecord::initFromFile(BamFileReader *bamFileReader)
 {
+	setFileIdx(bamFileReader->getFileIdx());
 	_bamAlignment = bamFileReader->getAlignment();
 	bamFileReader->getChrName(_chrName);
 

src/utils/FileRecordTools/Records/Bed3Interval.cpp

@@ -23,6 +23,7 @@ bool Bed3Interval::initFromFile(FileReader *fileReader)
 
 bool Bed3Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
 {
+	setFileIdx(fileReader->getFileIdx());
 	fileReader->getField(0, _chrName);
 	fileReader->getField(1, _startPosStr);
 	fileReader->getField(2, _endPosStr);

src/utils/FileRecordTools/Records/GffRecord.cpp

@@ -23,6 +23,7 @@ void GffRecord::clear()
 
 bool GffRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
 {
+	setFileIdx(fileReader->getFileIdx());
 	fileReader->getField(0, _chrName);
 	fileReader->getField(3, _startPosStr);
 	_startPos = str2chrPos(_startPosStr);

src/utils/FileRecordTools/Records/Makefile

@@ -17,12 +17,12 @@ INCLUDES = -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= RecordMgr.cpp RecordMgr.h Record.h Record.cpp EmptyRecord.h EmptyRecord.cpp Bed3Interval.h Bed3Interval.cpp \
+SOURCES= RecordMgr.cpp RecordMgr.h RecordList.h RecordList.cpp Record.h Record.cpp EmptyRecord.h EmptyRecord.cpp Bed3Interval.h Bed3Interval.cpp \
 	Bed4Interval.h Bed4Interval.cpp BedGraphInterval.h BedGraphInterval.cpp Bed5Interval.h Bed5Interval.cpp \
 	Bed6Interval.h Bed6Interval.cpp \
 	BedPlusInterval.h BedPlusInterval.cpp Bed12Interval.h Bed12Interval.cpp BamRecord.h BamRecord.cpp VcfRecord.h VcfRecord.cpp \
 	GffRecord.h GffRecord.cpp RecordKeyList.h RecordKeyList.cpp BlockMgr.h BlockMgr.cpp StrandQueue.h StrandQueue.cpp
-OBJECTS= RecordMgr.o Record.o EmptyRecord.o Bed3Interval.o Bed4Interval.o BedGraphInterval.o Bed5Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
+OBJECTS= RecordMgr.o RecordList.o Record.o EmptyRecord.o Bed3Interval.o Bed4Interval.o BedGraphInterval.o Bed5Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
 		VcfRecord.o GffRecord.o RecordKeyList.o BlockMgr.o StrandQueue.o
 _EXT_OBJECTS=ParseTools.o QuickString.o ChromIdLookup.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
@@ -38,7 +38,7 @@ $(BUILT_OBJECTS): $(SOURCES)
 
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/RecordMgr.o $(OBJ_DIR)/Record.o  $(OBJ_DIR)/EmptyRecord.o $(OBJ_DIR)/Bed3Interval.o $(OBJ_DIR)/Bed4Interval.o \
+	@rm -f $(OBJ_DIR)/RecordMgr.o $(OBJ_DIR)/RecordList.o $(OBJ_DIR)/Record.o  $(OBJ_DIR)/EmptyRecord.o $(OBJ_DIR)/Bed3Interval.o $(OBJ_DIR)/Bed4Interval.o \
 		$(OBJ_DIR)/BedGraphInterval.o $(OBJ_DIR)/Bed5Interval.o $(OBJ_DIR)/Bed6Interval.o \
 		$(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o $(OBJ_DIR)/StrandQueue.o
 

src/utils/FileRecordTools/Records/Record.cpp

@@ -3,7 +3,8 @@
 #include <cstdio>
 
 Record::Record()
-: _chrId(-1),
+: _fileIdx(-1),
+  _chrId(-1),
   _startPos(-1),