Merge pull request #41 from nkindlon/master

Refactored KeyListOps, Context, mapFile to make KeyListOps reusable by other tools

src/intersectFile/Makefile

@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
            -I$(UTILITIES_DIR)/FileRecordTools/ \
            -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
            -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+			-I$(UTILITIES_DIR)/KeyListOps/ \
            -I$(UTILITIES_DIR)/RecordOutputMgr/ \
            -I$(UTILITIES_DIR)/NewChromsweep \
            -I$(UTILITIES_DIR)/BinTree \

src/mapFile/mapFile.cpp

@@ -21,14 +21,11 @@ const int PRECISION = 21;
 FileMap::FileMap(ContextMap *context)
 : _context(context),
   _blockMgr(NULL),
-  _recordOutputMgr(NULL),
-  _colOps(_context->getColOps())
+  _recordOutputMgr(NULL)
 {
   _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
   _recordOutputMgr = new RecordOutputMgr();
   _recordOutputMgr->init(_context);
-  _keyListOps.setNullValue(_context->getNullValue());
-  _keyListOps.setDelimStr(_context->getDelim());
 }
 
 FileMap::~FileMap(void) {
@@ -46,174 +43,15 @@ bool FileMap::mapFiles()
     }
     RecordKeyList hitSet;
     while (sweep.next(hitSet)) {
-    	_outputValues.clear();
     	if (_context->getObeySplits()) {
 			RecordKeyList keySet(hitSet.getKey());
 			RecordKeyList resultSet(hitSet.getKey());
 			_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
-			calculateOutput(resultSet);
-			_recordOutputMgr->printRecord(resultSet.getKey(), _outputValues);
+			_recordOutputMgr->printRecord(resultSet.getKey(), _context->getColumnOpsVal(resultSet));
     	} else {
-			calculateOutput(hitSet);
-			_recordOutputMgr->printRecord(hitSet.getKey(), _outputValues);
+			_recordOutputMgr->printRecord(hitSet.getKey(), _context->getColumnOpsVal(hitSet));
 		}
     }
     return true;
 }
 
-void FileMap::calculateOutput(RecordKeyList &hits)
-{
-	//loop through all requested columns, and for each one, call the method needed
-	//for the operation specified.
-	_keyListOps.setKeyList(&hits);
-
-	double val = 0.0;
-	for (int i=0; i < (int)_colOps.size(); i++) {
-		int col = _colOps[i].first;
-		KeyListOps::OP_TYPES opCode = _colOps[i].second;
-
-		_keyListOps.setColumn(col);
-		switch (opCode) {
-		case KeyListOps::SUM:
-			val = _keyListOps.getSum();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::MEAN:
-			val = _keyListOps.getMean();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::STDDEV:
-			val = _keyListOps.getStddev();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::SAMPLE_STDDEV:
-			val = _keyListOps.getSampleStddev();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::MEDIAN:
-			val = _keyListOps.getMedian();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::MODE:
-			_outputValues.append(_keyListOps.getMode());
-			break;
-
-		case KeyListOps::ANTIMODE:
-			_outputValues.append(_keyListOps.getAntiMode());
-			break;
-
-		case KeyListOps::MIN:
-			val = _keyListOps.getMin();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::MAX:
-			val = _keyListOps.getMax();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::ABSMIN:
-			val = _keyListOps.getAbsMin();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::ABSMAX:
-			val = _keyListOps.getAbsMax();
-			if (isnan(val)) {
-				_outputValues.append(_context->getNullValue());
-			} else {
-				_outputValues.append(val);
-			}
-			break;
-
-		case KeyListOps::COUNT:
-			_outputValues.append(_keyListOps.getCount());
-			break;
-
-		case KeyListOps::DISTINCT:
-			_outputValues.append(_keyListOps.getDistinct());
-			break;
-
-		case KeyListOps::COUNT_DISTINCT:
-			_outputValues.append(_keyListOps.getCountDistinct());
-			break;
-
-		case KeyListOps::DISTINCT_ONLY:
-			_outputValues.append(_keyListOps.getDistinctOnly());
-			break;
-
-		case KeyListOps::COLLAPSE:
-			_outputValues.append(_keyListOps.getCollapse());
-			break;
-
-		case KeyListOps::CONCAT:
-			_outputValues.append(_keyListOps.getConcat());
-			break;
-
-		case KeyListOps::FREQ_ASC:
-			_outputValues.append(_keyListOps.getFreqAsc());
-			break;
-
-		case KeyListOps::FREQ_DESC:
-			_outputValues.append(_keyListOps.getFreqDesc());
-			break;
-
-		case KeyListOps::FIRST:
-			_outputValues.append(_keyListOps.getFirst());
-			break;
-
-		case KeyListOps::LAST:
-			_outputValues.append(_keyListOps.getLast());
-			break;
-
-		case KeyListOps::INVALID:
-		default:
-			// Any unrecognized operation should have been handled already in the context validation.
-			// It's thus unnecessary to handle it here, but throw an error to help us know if future
-			// refactoring or code changes accidentally bypass the validation phase.
-			cerr << "ERROR: Invalid operation given for column " << col << ". Exiting..." << endl;
-			break;
-		}
-		//if this isn't the last column, add a tab.
-		if (i < (int)_colOps.size() -1) {
-			_outputValues.append('\t');
-		}
-	}
-}

src/mapFile/mapFile.h

@@ -38,11 +38,6 @@ private:
     ContextMap *_context;
     BlockMgr *_blockMgr;
     RecordOutputMgr *_recordOutputMgr;
-    KeyListOps _keyListOps;
-    const ContextMap::colOpsType & _colOps;
-    QuickString _outputValues;  // placeholder for the results of mapping B to each a in A.
-
-    void calculateOutput(RecordKeyList &hits);
 };
 
 #endif /* MAPFILE_H */

src/nekSandbox1/Makefile

@@ -10,6 +10,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
 			-I$(UTILITIES_DIR)/FileRecordTools/ \
 		   -I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
            -I$(UTILITIES_DIR)/FileRecordTools/Records \
+ 			-I$(UTILITIES_DIR)/KeyListOps/ \
            -I$(UTILITIES_DIR)/general \
            -I$(UTILITIES_DIR)/NewChromsweep \
            -I$(UTILITIES_DIR)/GenomeFile/ \

src/regressTest/Makefile

@@ -18,6 +18,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/FileRecordTools/ \
 		   -I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
            -I$(UTILITIES_DIR)/FileRecordTools/Records \
+  			-I$(UTILITIES_DIR)/KeyListOps/ \
            -I$(UTILITIES_DIR)/general
 
 # ----------------------------------

src/sampleFile/Makefile

@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
            -I$(UTILITIES_DIR)/FileRecordTools/ \
            -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
            -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ 			-I$(UTILITIES_DIR)/KeyListOps/ \
           -I$(UTILITIES_DIR)/RecordOutputMgr/ \
             -I$(UTILITIES_DIR)/version/
 

src/utils/BinTree/Makefile

@@ -11,6 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/general/ \
            -I$(UTILITIES_DIR)/FileRecordTools/ \
            -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
            -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+			-I$(UTILITIES_DIR)/KeyListOps/ \
            -I$(UTILITIES_DIR)/BamTools/include \
            -I$(UTILITIES_DIR)/BamTools/src/ \
 	        -I$(UTILITIES_DIR)/version/

src/utils/Contexts/ContextBase.cpp

@@ -52,11 +52,16 @@ ContextBase::ContextBase()
   _hasConstantSeed(false),
   _seed(0),
   _forwardOnly(false),
-  _reverseOnly(false)
+  _reverseOnly(false),
+  _hasColumnOpsMethods(false)
 {
 	_programNames["intersect"] = INTERSECT;
 	_programNames["sample"] = SAMPLE;
 	_programNames["map"] = MAP;
+
+	if (hasColumnOpsMethods()) {
+		_keyListOps = new KeyListOps();
+	}
 }
 
 ContextBase::~ContextBase()
@@ -70,6 +75,11 @@ ContextBase::~ContextBase()
 		delete _files[i];
 		_files[i] = NULL;
 	}
+	if (hasColumnOpsMethods()) {
+		delete _keyListOps;
+		_keyListOps = NULL;
+	}
+
 }
 
 bool ContextBase::determineOutputType() {
@@ -167,6 +177,19 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-seed") == 0) {
 			if (!handle_seed()) return false;
         }
+        else if (strcmp(_argv[_i], "-o") == 0) {
+			if (!handle_o()) return false;
+        }
+        else if (strcmp(_argv[_i], "-c") == 0) {
+			if (!handle_c()) return false;
+        }
+        else if (strcmp(_argv[_i], "-null") == 0) {
+			if (!handle_null()) return false;
+        }
+        else if (strcmp(_argv[_i], "-delim") == 0) {
+			if (!handle_delim()) return false;
+        }
+
 	}
 	return true;
 }
@@ -182,6 +205,12 @@ bool ContextBase::isValidState()
 	if (!determineOutputType()) {
 		return false;
 	}
+	if (hasColumnOpsMethods()) {
+		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+		if (!_keyListOps->isValidColumnOps(dbFile)) {
+			return false;
+		}
+	}
 	return true;
 }
 
@@ -354,3 +383,85 @@ bool ContextBase::handle_ubam()
     markUsed(_i - _skipFirstArgs);
 	return true;
 }
+
+
+// Methods specific to column operations.
+// for col ops, -c is the string of columns upon which to operate
+bool ContextBase::handle_c()
+{
+	if (!hasColumnOpsMethods()) {
+		return false;
+	}
+    if ((_i+1) < _argc) {
+        _keyListOps->setColumns(_argv[_i + 1]);
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+    }
+    return true;
+}
+
+
+// for col ops, -o is the string of operations to apply to the columns (-c)
+bool ContextBase::handle_o()
+{
+	if (!hasColumnOpsMethods()) {
+		return false;
+	}
+    if ((_i+1) < _argc) {
+    	 _keyListOps->setOperations(_argv[_i + 1]);
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+    }
+    return true;
+}
+
+
+// for col ops, -null is a NULL vakue assigned
+// when no overlaps are detected.
+bool ContextBase::handle_null()
+{
+	if (!hasColumnOpsMethods()) {
+		return false;
+	}
+    if ((_i+1) < _argc) {
+    	 _keyListOps->setNullValue(_argv[_i + 1]);
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+    }
+    return true;
+}
+
+//for col ops, delimStr will appear between each item in
+//a collapsed but delimited list.
+bool ContextBase::handle_delim()
+{
+	if (!hasColumnOpsMethods()) {
+		return false;
+	}
+    if ((_i+1) < _argc) {
+    	 _keyListOps->setDelimStr(_argv[_i + 1]);
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+    }
+    return true;
+}
+
+void ContextBase::setColumnOpsMethods(bool val)
+{
+	_hasColumnOpsMethods = val;
+	if (val) {
+		_keyListOps = new KeyListOps();
+	}
+}
+
+const QuickString &ContextBase::getColumnOpsVal(RecordKeyList &keyList) const {
+	if (!hasColumnOpsMethods()) {
+		return _nullStr;
+	}
+	return _keyListOps->getOpVals(keyList);
+}
+

src/utils/Contexts/ContextBase.h

@@ -24,6 +24,7 @@
 #include "NewGenomeFile.h"
 #include "api/BamReader.h"
 #include "api/BamAux.h"
+#include "KeyListOps.h"
 
 
 class ContextBase {
@@ -144,6 +145,13 @@ public:
     //methods.
     virtual bool hasIntersectMethods() const { return false; }
 
+    // determine whether column operations like those used in map
+    // are available.
+    void setColumnOpsMethods(bool val);
+    virtual bool hasColumnOpsMethods() const { return _hasColumnOpsMethods; }
+    const QuickString &getColumnOpsVal(RecordKeyList &keyList) const;
+    //methods applicable only to column operations.
+
 protected:
 	PROGRAM_TYPE _program;
 
@@ -204,6 +212,10 @@ protected:
 	bool _forwardOnly;
 	bool _reverseOnly;
 
+	bool _hasColumnOpsMethods;
+	KeyListOps *_keyListOps;
+	QuickString _nullStr; //placeholder return value when col ops aren't valid.
+
 	void markUsed(int i) { _argsProcessed[i] = true; }
 	bool isUsed(int i) const { return _argsProcessed[i]; }
 	bool cmdArgsValid();
@@ -227,6 +239,11 @@ protected:
 	virtual bool handle_split();
 	virtual bool handle_sorted();
 	virtual bool handle_ubam();
+
+	virtual bool handle_c();
+	virtual bool handle_o();
+	virtual bool handle_null();
+	virtual bool handle_delim();
 };
 
 #endif /* CONTEXTBASE_H_ */

src/utils/Contexts/ContextMap.cpp

@@ -8,18 +8,11 @@
 #include "ContextMap.h"
 
 ContextMap::ContextMap()
-: _delimStr(",")
 {
 	// map requires sorted input
 	setSortedInput(true);
 	setLeftJoin(true);
-
-	// default to BED score column
-	setColumns("5");
-	// default to "sum"
-	setOperations("sum");
-	// default to "." as a NULL value
-	setNullValue('.');
+	setColumnOpsMethods(true);
 }
 
 ContextMap::~ContextMap()
@@ -45,131 +38,22 @@ bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
 		if (isUsed(_i - _skipFirstArgs)) {
 			continue;
 		}
-        else if (strcmp(_argv[_i], "-o") == 0) {
-			if (!handle_o()) return false;
-        }
-        else if (strcmp(_argv[_i], "-c") == 0) {
-			if (!handle_c()) return false;
-        }
-        else if (strcmp(_argv[_i], "-null") == 0) {
-			if (!handle_null()) return false;
-        }
-        else if (strcmp(_argv[_i], "-delim") == 0) {
-			if (!handle_delim()) return false;
-        }
+		if (strcmp(_argv[_i], "-c") == 0) {
+			//bypass intersect's use of the -c option, because -c
+			//means writeCount for intersect, but means columns for map.
+			if (!ContextBase::handle_c()) return false;
+		}
 
 	}
 	return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
 }
-
-
-bool ContextMap::isValidState()
-{
-	if (!ContextIntersect::isValidState()) {
-		return false;
-	}
-
-    if (getDatabaseFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
-         //throw Error
-        cerr << endl << "*****" << endl
-             << "***** ERROR: BAM database file not currently supported for the map tool." 
-             << endl;
-        exit(1);
-    }
-
-
-	//get the strings from context containing the comma-delimited lists of columns
-	//and operations. Split both of these into vectors. Get the operation code
-	//for each operation string. Finally, make a vector of pairs, where the first
-	//member of each pair is a column number, and the second member is the code for the
-	//operation to perform on that column.
-
-	vector<QuickString> columnsVec;
-	vector<QuickString> opsVec;
-	int numCols = Tokenize(_columns, columnsVec, ',');
-	int numOps = Tokenize(_operations, opsVec, ',');
-
-	if (numOps < 1 || numCols < 1) {
-		 cerr << endl << "*****" << endl
-		             << "***** ERROR: There must be at least one column and at least one operation named." << endl;
-		 return false;
-	}
-	if (numOps > 1 && numCols != numOps) {
-		 cerr << endl << "*****" << endl
-		             << "***** ERROR: There are " << numCols <<" columns given, but there are " << numOps << " operations. " << endl;
-		cerr << "\tPlease provide either a single operation that will be applied to all listed columns, " << endl;
-		cerr << "\tor an operation for each column." << endl;
-		return false;
-	}
-	KeyListOps keyListOps;
-	for (int i=0; i < (int)columnsVec.size(); i++) {
-		int col = str2chrPos(columnsVec[i]);
-
-		//check that the column number is valid
-		if (col < 1 || col > getDatabaseFile()->getNumFields()) {
-			 cerr << endl << "*****" << endl  << "***** ERROR: Requested column " << col << ", but database file "
-					 << getDatabaseFileName() << " only has fields 1 - " << getDatabaseFile()->getNumFields() << "." << endl;
-			 return false;
-		}
-		const QuickString &operation = opsVec.size() > 1 ? opsVec[i] : opsVec[0];
-		KeyListOps::OP_TYPES opCode = keyListOps.getOpCode(operation);
-		if (opCode == KeyListOps::INVALID) {
-			cerr << endl << "*****" << endl
-								 << "***** ERROR: " << operation << " is not a valid operation. " << endl;
-			return false;
-		}
-		_colOps.push_back(pair<int, KeyListOps::OP_TYPES>(col, opCode));
-	}
-    return true;
-}
-
-
-// for map, -c is the string of columns upon which to operate
-bool ContextMap::handle_c()
-{
-    if ((_i+1) < _argc) {
-        setColumns(_argv[_i + 1]);
-        markUsed(_i - _skipFirstArgs);
-        _i++;
-        markUsed(_i - _skipFirstArgs);
-    }
-    return true;
-}
-
-
-// for map, -o is the string of operations to apply to the columns (-c)
-bool ContextMap::handle_o()
-{
-    if ((_i+1) < _argc) {
-        setOperations(_argv[_i + 1]);
-        markUsed(_i - _skipFirstArgs);
-        _i++;
-        markUsed(_i - _skipFirstArgs);
-    }
-    return true;
-}
-
-
-// for map, -null is a NULL vakue assigned
-// when no overlaps are detected.
-bool ContextMap::handle_null()
-{
-    if ((_i+1) < _argc) {
-        setNullValue(_argv[_i + 1]);
-        markUsed(_i - _skipFirstArgs);
-        _i++;
-        markUsed(_i - _skipFirstArgs);
-    }
-    return true;
-}
-
-bool ContextMap::handle_delim()
-{
-    if ((_i+1) < _argc) {
-    	_delimStr = _argv[_i + 1];
-        markUsed(_i - _skipFirstArgs);
-        _i++;
-        markUsed(_i - _skipFirstArgs);
-    }
-    return true;
-}
+//
+//
+//bool ContextMap::isValidState()
+//{
+//	if (!ContextIntersect::isValidState()) {
+//		return false;
+//	}
+//}
+//
+//

src/utils/Contexts/ContextMap.h

@@ -15,37 +15,14 @@ class ContextMap : public ContextIntersect {
 public:
 	ContextMap();
 	virtual ~ContextMap();
-	virtual bool isValidState();
-
+//	virtual bool isValidState();
+//
 	virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
-
-	const QuickString &getColumns() const { return _columns; }
-	void setColumns(const QuickString &columns) { _columns = columns; }
-
-	const QuickString & getOperations() const { return _operations; }
-	void setOperations(const QuickString & operation) { _operations = operation; }
-
-	const QuickString & getNullValue() const { return _nullValue; }
-	void setNullValue(const QuickString & nullValue) { _nullValue = nullValue; }
-
-	const QuickString &getDelim() const { return _delimStr; }
+//
     virtual bool hasIntersectMethods() const { return true; }
-
-    typedef vector<pair<int, KeyListOps::OP_TYPES> > colOpsType;
-	const colOpsType &getColOps() const { return _colOps; }
+//
 
 private:
-    QuickString _operations;
-    QuickString _columns;
-    QuickString _nullValue;
-    KeyListOps _keyListOps;
-    colOpsType _colOps;
-    QuickString _delimStr;
-
-	virtual bool handle_c();
-	virtual bool handle_o();
-	virtual bool handle_null();
-	virtual bool handle_delim();
 
 };
 

src/utils/FileRecordTools/Records/BamRecord.cpp

@@ -172,5 +172,10 @@ const QuickString &BamRecord::getField(int fieldNum) const
 	return Bed6Interval::getField(fieldNum);
 }
 
+bool BamRecord::isNumericField(int fieldNum) {
+
+	//TBD: As with getField, this isn't defined for BAM.
+	return (fieldNum > 6 ? false : Bed6Interval::isNumericField(fieldNum));
+}
 
 

src/utils/FileRecordTools/Records/BamRecord.h

@@ -40,6 +40,7 @@ public:
 
 	virtual const QuickString &getField(int fieldNum) const;
 	virtual int getNumFields() const  { return 12; }
+	static bool isNumericField(int fieldNum);
 
 protected:
 	BamTools::BamAlignment _bamAlignment;

src/utils/FileRecordTools/Records/Bed12Interval.cpp

@@ -146,3 +146,29 @@ const QuickString &Bed12Interval::getField(int fieldNum) const
 	}
 }
 
+bool Bed12Interval::isNumericField(int fieldNum) {
+	switch (fieldNum) {
+	case 7:
+		return true;
+		break;
+	case 8:
+		return true;
+		break;
+	case 9:
+		return false;
+		break;
+	case 10:
+		return true;
+		break;
+	case 11:
+		return false;
+		break;
+	case 12:
+		return false;
+		break;
+	default:
+		return Bed6Interval::isNumericField(fieldNum);
+		break;
+	}
+}
+

src/utils/FileRecordTools/Records/Bed12Interval.h

@@ -54,6 +54,7 @@ public:
 
 	virtual const QuickString &getField(int fieldNum) const;
 	virtual int getNumFields() const  { return 12; }
+	static bool isNumericField(int fieldNum);
 
 
 protected:

src/utils/FileRecordTools/Records/Bed3Interval.cpp

@@ -79,3 +79,23 @@ const QuickString &Bed3Interval::getField(int fieldNum) const
 		break;
 	}
 }
+
+bool Bed3Interval::isNumericField(int fieldNum) {
+	switch (fieldNum) {
+	case 1:
+		return false; //chrom
+		break;
+	case 2:
+		return true; //startPos
+		break;
+	case 3:
+		return true; //endPos
+		break;
+	default:
+	    cerr << endl << "*****" << endl
+	         << "*****ERROR: requested invalid column " << fieldNum << ". Exiting." << endl
+	          << endl << "*****" << endl;
+	    exit(1);
+	    break;
+	}
+}

src/utils/FileRecordTools/Records/Bed3Interval.h

@@ -32,6 +32,8 @@ public:
 	virtual const QuickString &getField(int fieldNum) const;
 	virtual int getNumFields() const  { return 3; }
 
+	static bool isNumericField(int fieldNum);
+
 protected:
 	virtual ~Bed3Interval();
 

src/utils/FileRecordTools/Records/Bed4Interval.cpp

@@ -60,3 +60,8 @@ const QuickString &Bed4Interval::getField(int fieldNum) const
 	}
 }
 
+bool Bed4Interval::isNumericField(int fieldNum) {
+	return (fieldNum == 4 ? false : Bed3Interval::isNumericField(fieldNum));
+}
+
+

src/utils/FileRecordTools/Records/Bed4Interval.h

@@ -28,6 +28,7 @@ public:
 
 	virtual const QuickString &getField(int fieldNum) const;
 	virtual int getNumFields() const  { return 4; }
+	static bool isNumericField(int fieldNum);
 
 
 protected:

src/utils/FileRecordTools/Records/Bed5Interval.cpp

@@ -70,3 +70,16 @@ const QuickString &Bed5Interval::getField(int fieldNum) const
 		break;
 	}
 }
+
+bool Bed5Interval::isNumericField(int fieldNum) {
+	switch (fieldNum) {
+	case 4:
+		return false;
+		break;
+	case 5:
+		return true;
+		break;
+	default:
+		return Bed3Interval::isNumericField(fieldNum);
+	}
+}