Refactored KeyListOps, Context, mapFile for KeyListOps re-usability 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/Makefile

@@ -29,6 +29,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
            -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
            -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
            -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+			-I$(UTILITIES_DIR)/KeyListOps/ \
            -I$(UTILITIES_DIR)/NewChromsweep \
            -I$(UTILITIES_DIR)/VectorOps \
            -I$(UTILITIES_DIR)/BinTree \

src/mapFile/mapFile.cpp

@@ -47,74 +47,11 @@ bool FileMap::mapFiles()
 			RecordKeyList keySet(hitSet.getKey());
 			RecordKeyList resultSet(hitSet.getKey());
 			_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
-			SummarizeHits(resultSet);
-			_recordOutputMgr->printRecord(resultSet.getKey(), _output);
+			_recordOutputMgr->printRecord(resultSet.getKey(), _context->getColumnOpsVal(resultSet));
     	} else {
-			SummarizeHits(hitSet);
-			_recordOutputMgr->printRecord(hitSet.getKey(), _output);
+			_recordOutputMgr->printRecord(hitSet.getKey(), _context->getColumnOpsVal(hitSet));
 		}
     }
     return true;
 }
 
-void FileMap::ExtractColumnFromHits(RecordKeyList &hits) {
-  _column_vec.clear();
-  RecordKeyList::const_iterator_type iter = hits.begin();
-  for (; iter != hits.end(); iter = hits.next()) 
-  {
-    _column_vec.push_back(iter->value()->getField(_context->getColumn()).str());
-  }
-} 
-
-void FileMap::SummarizeHits(RecordKeyList &hits) {
-
-    const QuickString & operation = _context->getColumnOperation();
-    _output.clear();
-
-    if (hits.size() == 0) {
-        if (operation == "count" || operation == "count_distinct")
-            _output.append("0");
-        else
-            _output.append(_context->getNullValue().str());
-        return;
-    } 
-
-    _tmp_output.str("");
-    _tmp_output.clear();
-
-    ExtractColumnFromHits(hits);
-
-    VectorOps vo(_column_vec);
-    if (operation == "sum") 
-        _tmp_output << setprecision (PRECISION) << vo.GetSum();
-    else if (operation == "mean")
-        _tmp_output << setprecision (PRECISION) << vo.GetMean();
-    else if (operation == "median")
-        _tmp_output << setprecision (PRECISION) << vo.GetMedian();
-    else if (operation == "min")
-        _tmp_output << setprecision (PRECISION) << vo.GetMin();
-    else if (operation == "max")
-        _tmp_output << setprecision (PRECISION) << vo.GetMax();
-    else if (operation == "absmin")
-        _tmp_output << setprecision (PRECISION) << vo.GetAbsMin();
-    else if (operation == "absmax")
-        _tmp_output << setprecision (PRECISION) << vo.GetAbsMax();
-    else if (operation == "mode")
-        _tmp_output << vo.GetMode();
-    else if (operation == "antimode")
-        _tmp_output << vo.GetAntiMode();
-    else if (operation == "count") 
-        _tmp_output << setprecision (PRECISION) << vo.GetCount();
-    else if (operation == "count_distinct")
-        _tmp_output << setprecision (PRECISION) << vo.GetCountDistinct();
-    else if (operation == "collapse")
-        _tmp_output << vo.GetCollapse();
-    else if (operation == "distinct")
-        _tmp_output << vo.GetDistinct();
-    else {
-        cerr << "ERROR: " << operation << " is an unrecognized operation\n";
-        exit(1);
-    }
-    _output.append(_tmp_output.str());
-
-}

src/mapFile/mapFile.h

@@ -18,10 +18,11 @@ using namespace std;
 #include <iomanip>
 #include "VectorOps.h"
 #include "RecordKeyList.h"
+#include "KeyListOps.h"
+#include "ContextMap.h"
 
 using namespace std;
 
-class ContextMap;
 class BlockMgr;
 class RecordOutputMgr;
 
@@ -35,90 +36,8 @@ public:
 
 private:
     ContextMap *_context;
-    Record *_queryRec;
-    Record *_databaseRec;
     BlockMgr *_blockMgr;
     RecordOutputMgr *_recordOutputMgr;
-
-    vector<string> _column_vec; // vector to hold current column's worth of data
-
-    ostringstream _tmp_output;
-    QuickString _output;  // placeholder for the results of mapping B to each a in A.
-    //------------------------------------------------
-    // private methods
-    //------------------------------------------------
-    void Map();
-    void SummarizeHits(RecordKeyList &hits);
-    void ExtractColumnFromHits(RecordKeyList &hits);
-
 };
 
 #endif /* MAPFILE_H */
-
-
-/*
-#include "bedFile.h"
-#include "chromsweep.h"
-#include "VectorOps.h"
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-
-#include <vector>
-#include <iostream>
-#include <algorithm>
-#include <numeric>
-#include <fstream>
-#include <iomanip>
-#include <stdlib.h>
-using namespace std;
-
-
-
-class BedMap {
-
-public:
-
-    // constructor
-    BedMap(string bedAFile, string bedBFile, int column, string operation,
-                   float overlapFraction, bool sameStrand, 
-                   bool diffStrand, bool reciprocal, 
-                   bool choseNullValue, string nullValue, 
-                   bool printHeader);
-
-    // destructor
-    ~BedMap(void);
-
-private:
-
-    //------------------------------------------------
-    // private attributes
-    //------------------------------------------------
-    string _bedAFile;
-    string _bedBFile;
-    int _column;
-    string _operation;
-    bool  _sameStrand;
-    bool  _diffStrand;
-    bool  _reciprocal;
-    float _overlapFraction;
-    string _nullValue;
-    bool  _printHeader;
-    
-    // instance of a bed file class.
-    BedFile *_bedA, *_bedB;
-    
-    vector<string> _column_vec; // vector to hold current column's worth of data
-
-    //------------------------------------------------
-    // private methods
-    //------------------------------------------------
-    void Map();
-    string MapHits(const BED &a, const vector<BED> &hits);
-    void ExtractColumnFromHits(const vector<BED> &hits);
-};
-*/
-//#endif /* MAPFILE_H */

src/mapFile/mapMain.cpp

@@ -38,144 +38,6 @@ int map_main(int argc, char* argv[]) {
     return retVal ? 0 : 1;
 }
 
-
-/*
-int map_main(int argc, char* argv[]) {
-
-    // our configuration variables
-    bool showHelp = false;
-
-    // input files
-    string bedAFile;
-    string bedBFile;
-    int column = 5;
-    string operation = "sum";
-    string nullValue = ".";
-
-    // input arguments
-    float overlapFraction = 1E-9;
-
-    bool haveBedA           = false;
-    bool haveBedB           = false;
-    bool haveColumn         = false;
-    bool haveOperation      = false;
-    bool haveFraction       = false;
-    bool reciprocalFraction = false;
-    bool sameStrand         = false;
-    bool diffStrand         = false;
-    bool printHeader        = false;
-    bool choseNullValue     = false;
-
-    // check to see if we should print out some help
-    if(argc <= 1) showHelp = true;
-
-    for(int i = 1; i < argc; i++) {
-        int parameterLength = (int)strlen(argv[i]);
-
-        if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
-        (PARAMETER_CHECK("--help", 5, parameterLength))) {
-            showHelp = true;
-        }
-    }
-
-    if(showHelp) map_help();
-
-    // do some parsing (all of these parameters require 2 strings)
-    for(int i = 1; i < argc; i++) {
-
-        int parameterLength = (int)strlen(argv[i]);
-
-        if(PARAMETER_CHECK("-a", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBedA = true;
-                bedAFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBedB = true;
-                bedBFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveColumn = true;
-                column = atoi(argv[i + 1]);
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-o", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveOperation = true;
-                operation = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFraction = true;
-                overlapFraction = atof(argv[i + 1]);
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
-            reciprocalFraction = true;
-        }
-        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
-            sameStrand = true;
-        }
-        else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
-            diffStrand = true;
-        }
-        else if (PARAMETER_CHECK("-null", 5, parameterLength)) {
-            nullValue = argv[i + 1];
-            choseNullValue = true;
-            i++;
-        }
-        else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
-            printHeader = true;
-        }
-        else {
-            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have both input files
-    if (!haveBedA || !haveBedB) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (reciprocalFraction && !haveFraction) {
-        cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (sameStrand && diffStrand) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-
-        BedMap *bm = new BedMap(bedAFile, bedBFile, column, operation,
-                                       overlapFraction, sameStrand,
-                                       diffStrand, reciprocalFraction,
-                                       choseNullValue, nullValue, 
-                                       printHeader);
-        delete bm;
-        return 0;
-    }
-    else {
-        map_help();
-        return 0;
-    }
-}
-*/
-
 void map_help(void) {
 
     cerr << "\nTool:    bedtools map (aka mapBed)" << endl;

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

@@ -52,20 +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;
 
-	_validScoreOps.insert("sum");
-	_validScoreOps.insert("max");
-	_validScoreOps.insert("min");
-	_validScoreOps.insert("mean");
-	_validScoreOps.insert("mode");
-	_validScoreOps.insert("median");
-	_validScoreOps.insert("antimode");
-	_validScoreOps.insert("collapse");
+	if (hasColumnOpsMethods()) {
+		_keyListOps = new KeyListOps();
+	}
 }
 
 ContextBase::~ContextBase()
@@ -79,6 +75,11 @@ ContextBase::~ContextBase()
 		delete _files[i];
 		_files[i] = NULL;
 	}
+	if (hasColumnOpsMethods()) {
+		delete _keyListOps;
+		_keyListOps = NULL;
+	}
+
 }
 
 bool ContextBase::determineOutputType() {
@@ -176,6 +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;
 }
@@ -191,6 +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;
 }
 
@@ -363,3 +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;
 
@@ -191,15 +199,11 @@ protected:
     int _bamHeaderAndRefIdx;
     int _maxNumDatabaseFields;
     bool _useFullBamTags;
-    QuickString _columnOperation;
-    int _column;
-    QuickString _nullValue;
 	bool _reportCount;
 	int _maxDistance;
 	bool _reportNames;
 	bool _reportScores;
 	QuickString _scoreOp;
-	set<QuickString> _validScoreOps;
 
 	int _numOutputRecords;
 
@@ -208,6 +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();
@@ -231,6 +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/ContextIntersect.h

@@ -21,6 +21,8 @@ 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); }
     int getQueryFileIdx() const { return _queryFileIdx; }
 	void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
 	int getDatabaseFileIdx() const { return _databaseFileIdx; }

src/utils/Contexts/ContextMap.cpp

@@ -12,13 +12,7 @@ ContextMap::ContextMap()
 	// map requires sorted input
 	setSortedInput(true);
 	setLeftJoin(true);
-
-	// default to BED score column
-	setColumn(5);
-	// default to "sum"
-	setColumnOperation("sum");
-	// default to "." as a NULL value
-	setNullValue('.');
+	setColumnOpsMethods(true);
 }
 
 ContextMap::~ContextMap()
@@ -44,75 +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;
-        }
-	}
-	return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
-}
-
+		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;
+		}
 
-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);
-    }
-	// TODO 
-	// enforce any specific checks for Map.
-    return true;
-}
-
-
-// for map, -c is the column upon which to operate
-bool ContextMap::handle_c()
-{
-    if ((_i+1) < _argc) {
-        setColumn(atoi(_argv[_i + 1]));
-        markUsed(_i - _skipFirstArgs);
-        _i++;
-        markUsed(_i - _skipFirstArgs);
-    }
-    return true;
-}
-
-
-// for map, -o is the operation to apply to the column (-c)
-bool ContextMap::handle_o()
-{
-    if ((_i+1) < _argc) {
-        setColumnOperation(_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;
+	return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
 }
+//
+//
+//bool ContextMap::isValidState()
+//{
+//	if (!ContextIntersect::isValidState()) {
+//		return false;
+//	}
+//}
+//
+//

src/utils/Contexts/ContextMap.h

@@ -9,30 +9,20 @@
 #define CONTEXTMAP_H_
 
 #include "ContextIntersect.h"
+#include "KeyListOps.h"
 
 class ContextMap : public ContextIntersect {
 public:
 	ContextMap();
 	virtual ~ContextMap();
-	virtual bool isValidState();
-
+//	virtual bool isValidState();
+//
 	virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
-
-	int getColumn() const { return _column; }
-	void setColumn(int column) { _column = column; }
-
-	const QuickString & getColumnOperation() const { return _columnOperation; }
-	void setColumnOperation(const QuickString & operation) { _columnOperation = operation; }
-
-	const QuickString & getNullValue() const { return _nullValue; }
-	void setNullValue(const QuickString & nullValue) { _nullValue = nullValue; }
-
+//
     virtual bool hasIntersectMethods() const { return true; }
+//
 
 private:
-	virtual bool handle_c();
-	virtual bool handle_o();
-	virtual bool handle_null();
 
 };
 

src/utils/Contexts/Makefile

@@ -9,6 +9,7 @@ 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)/GenomeFile/ \
  			-I$(UTILITIES_DIR)/BamTools/include \
 			-I$(UTILITIES_DIR)/BamTools/src/ \

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;
+	}
+}