first pass at using Context and PFM for the map tool.

Makefile

@@ -46,7 +46,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/jaccard \
 		  $(SRC_DIR)/linksBed \
 		  $(SRC_DIR)/maskFastaFromBed \
-		  $(SRC_DIR)/mapBed \
+		  $(SRC_DIR)/mapFile \
 		  $(SRC_DIR)/mergeBed \
 		  $(SRC_DIR)/multiBamCov \
 		  $(SRC_DIR)/multiIntersectBed \

src/mapBed/Makefile → src/mapFile/Makefile

@@ -5,22 +5,39 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
-           -I$(UTILITIES_DIR)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/fileType/ \
+# INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+#            -I$(UTILITIES_DIR)/gzstream/ \
+#            -I$(UTILITIES_DIR)/genomeFile/ \
+#            -I$(UTILITIES_DIR)/lineFileUtilities/ \
+#            -I$(UTILITIES_DIR)/fileType/ \
+#            -I$(UTILITIES_DIR)/BamTools/include \
+#            -I$(UTILITIES_DIR)/BamTools-Ancillary \
+#            -I$(UTILITIES_DIR)/chromsweep \
+#            -I$(UTILITIES_DIR)/VectorOps \
+#            -I$(UTILITIES_DIR)/version/
+
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+			-I$(UTILITIES_DIR)/general/ \
+			-I$(UTILITIES_DIR)/fileType/ \
+			-I$(UTILITIES_DIR)/gzstream/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/BamTools/include \
+           -I$(UTILITIES_DIR)/BamTools/src \
+           -I$(UTILITIES_DIR)/BlockedIntervals \
            -I$(UTILITIES_DIR)/BamTools-Ancillary \
-           -I$(UTILITIES_DIR)/chromsweep \
+           -I$(UTILITIES_DIR)/FileRecordTools/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+           -I$(UTILITIES_DIR)/NewChromsweep \
            -I$(UTILITIES_DIR)/VectorOps \
+           -I$(UTILITIES_DIR)/BinTree \
            -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= mapMain.cpp mapBed.cpp mapBed.h
-OBJECTS= mapMain.o mapBed.o
+SOURCES= mapMain.cpp mapFile.cpp mapFile.h
+OBJECTS= mapMain.o mapFile.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 all: $(BUILT_OBJECTS)
@@ -33,6 +50,6 @@ $(BUILT_OBJECTS): $(SOURCES)
 
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/mapMain.o $(OBJ_DIR)/mapBed.o
+	@rm -f $(OBJ_DIR)/mapMain.o $(OBJ_DIR)/mapFile.o
 
 .PHONY: clean

src/mapBed/mapBed.cpp → src/mapFile/mapFile.cpp

@@ -9,9 +9,127 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-#include "lineFileUtilities.h"
-#include "mapBed.h"
+#include "mapFile.h"
+#include "ContextMap.h"
+#include "FileRecordMgr.h"
+#include "NewChromsweep.h"
+#include "BinTree.h"
+#include "RecordOutputMgr.h"
 
+const int PRECISION = 21;
+
+FileMap::FileMap(ContextMap *context)
+: _context(context),
+  _blockMgr(NULL),
+  _recordOutputMgr(NULL)
+{
+  // FIX ME - block manager only works for intersect
+  //_blockMgr = new BlockMgr();
+  //_blockMgr->setContext(context);
+  _recordOutputMgr = new RecordOutputMgr();
+}
+
+FileMap::~FileMap(void) {
+  if (_blockMgr != NULL) {
+    delete _blockMgr;
+    _blockMgr = NULL;
+  }
+  delete _recordOutputMgr;
+}
+
+bool FileMap::mapFiles()
+{
+    NewChromSweep sweep(_context);
+    if (!sweep.init()) {
+      return false;
+    }
+    if (!_recordOutputMgr->init(_context)) {
+      return false;
+    }
+    RecordKeyList hitSet;
+    while (sweep.next(hitSet)) {
+      //if (_context->getObeySplits()) {
+      //  RecordKeyList keySet(hitSet.getKey());
+      //  RecordKeyList resultSet(hitSet.getKey());
+      //  _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+      //} else {
+      //}
+      //_recordOutputMgr->printKeyAndTerminate(hitSet);
+      _recordOutputMgr->printRecord(hitSet.getKey(), MapHits(hitSet));
+    }
+    return true;
+}
+
+void FileMap::ExtractColumnFromHits(RecordKeyList &hits) {
+  for (RecordKeyList::const_iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) {
+      try {
+        ostringstream startString;
+        startString << iter->value()->getStartPos();
+        //_column_vec.push_back(iter->value().fields.at(_column));
+        _column_vec.push_back(startString.str());
+      }
+      catch(std::out_of_range& e) {
+        exit(1);
+      }
+      /*
+      catch(std::out_of_range& e) {
+        cerr << endl << "*****" << endl 
+             << "*****ERROR: requested column ("
+             << _column + 1
+             << ") exceeds the number of columns in file at line "
+             << _bedA->_lineNum << ". Exiting." 
+             << endl << "*****" << endl;
+        exit(1);
+      }
+      */
+  }
+}
+
+string FileMap::MapHits(RecordKeyList &hits) {
+    
+    ostringstream output;
+    if (hits.size() == 0)
+        // FIX ME
+        return "-1";
+        //return _nullValue;
+
+    ExtractColumnFromHits(hits);
+
+    string operation = _context->getColumnOperation();
+
+    VectorOps vo(_column_vec);
+    if (operation == "sum") 
+        output << setprecision (PRECISION) << vo.GetSum();
+    else if (operation == "mean")
+        output << setprecision (PRECISION) << vo.GetMean();
+    else if (operation == "median")
+        output << setprecision (PRECISION) << vo.GetMedian();
+    else if (operation == "min")
+        output << setprecision (PRECISION) << vo.GetMin();
+    else if (operation == "max")
+        output << setprecision (PRECISION) << vo.GetMax();
+    else if (operation == "mode")
+        output << vo.GetMode();
+    else if (operation == "antimode")
+        output << vo.GetAntiMode();
+    else if (operation == "count") 
+        output << setprecision (PRECISION) << vo.GetCount();
+    else if (operation == "count_distinct")
+        output << setprecision (PRECISION) << vo.GetCountDistinct();
+    else if (operation == "collapse")
+        output << vo.GetCollapse();
+    else if (operation == "distinct")
+        output << vo.GetDistinct();
+    else {
+        cerr << "ERROR: " << operation << " is an unrecoginzed operation\n";
+        exit(1);
+    }
+    _column_vec.clear();
+    return output.str();
+}
+
+
+/*
 const int PRECISION = 21;
 double GetUserColumn(const string s);
 
@@ -120,3 +238,4 @@ void BedMap::ExtractColumnFromHits(const vector<BED> &hits) {
         }
     }
 }
+*/

src/mapBed/mapBed.h → src/mapFile/mapFile.h

 /*****************************************************************************
-  mapBed.h
+  mapFile.h
 
   (c) 2009 - Aaron Quinlan
   Hall Laboratory
@@ -9,9 +9,52 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-#ifndef MAPBED_H
-#define MAPBED_H
+#ifndef MAPFILE_H
+#define MAPFILE_H
 
+using namespace std;
+
+#include <sstream>
+#include <iomanip>
+#include "VectorOps.h"
+#include "RecordKeyList.h"
+
+using namespace std;
+
+class ContextMap;
+class BlockMgr;
+class RecordOutputMgr;
+
+class FileMap {
+
+public:
+    FileMap(ContextMap *context);
+    ~FileMap(void);
+
+    bool mapFiles();
+
+private:
+    ContextMap *_context;
+    Record *_queryRec;
+    Record *_databaseRec;
+    BlockMgr *_blockMgr;
+    RecordOutputMgr *_recordOutputMgr;
+
+    vector<string> _column_vec; // vector to hold current column's worth of data
+
+    //------------------------------------------------
+    // private methods
+    //------------------------------------------------
+    void Map();
+    string MapHits(RecordKeyList &hits);
+    void ExtractColumnFromHits(RecordKeyList &hits);
+
+};
+
+#endif /* MAPFILE_H */
+
+
+/*
 #include "bedFile.h"
 #include "chromsweep.h"
 #include "VectorOps.h"
@@ -75,5 +118,5 @@ private:
     string MapHits(const BED &a, const vector<BED> &hits);
     void ExtractColumnFromHits(const vector<BED> &hits);
 };
-
-#endif /* MAPBED_H */
+*/
+//#endif /* MAPFILE_H */

src/mapBed/mapMain.cpp → src/mapFile/mapMain.cpp

@@ -9,21 +9,37 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-#include "mapBed.h"
-#include "version.h"
-
 using namespace std;
 
+#include "mapFile.h"
+#include "ContextMap.h"
+
 // define our program name
 #define PROGRAM_NAME "bedtools map"
 
+void map_help(void);
 
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+int map_main(int argc, char* argv[]) {
+
+    ContextMap *context = new ContextMap();
+    if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+        if (!context->getErrorMsg().empty()) {
+            cerr << context->getErrorMsg() << endl;
+        }
+        map_help();
+        delete context;
+        return 0;
+    }
+    FileMap *fileMap = new FileMap(context);
+
+    bool retVal = fileMap->mapFiles();
+    delete fileMap;
+    delete context;
+    return retVal ? 0 : 1;
+}
 
-// function declarations
-void map_help(void);
 
+/*
 int map_main(int argc, char* argv[]) {
 
     // our configuration variables
@@ -158,6 +174,7 @@ int map_main(int argc, char* argv[]) {
         return 0;
     }
 }
+*/
 
 void map_help(void) {
 

src/utils/Contexts/ContextBase.cpp

@@ -55,6 +55,7 @@ ContextBase::ContextBase()
 {
 	_programNames["intersect"] = INTERSECT;
 	_programNames["sample"] = SAMPLE;
+	_programNames["map"] = MAP;
 
 	_validScoreOps.insert("sum");
 	_validScoreOps.insert("max");

src/utils/Contexts/ContextBase.h

@@ -210,7 +210,8 @@ protected:
     int _bamHeaderAndRefIdx;
     int _maxNumDatabaseFields;
     bool _useFullBamTags;
-
+    string _columnOperation;
+    int _column;
 	bool _reportCount;
 	int _maxDistance;
 	bool _reportNames;

src/utils/Contexts/Makefile

@@ -15,8 +15,8 @@ INCLUDES =  -I$(UTILITIES_DIR)/general/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= ContextBase.cpp ContextBase.h ContextIntersect.cpp ContextIntersect.h ContextSample.cpp ContextSample.h
-OBJECTS= ContextBase.o ContextIntersect.o ContextSample.o
+SOURCES= ContextBase.cpp ContextBase.h ContextIntersect.cpp ContextIntersect.h ContextMap.cpp ContextMap.h ContextSample.cpp ContextSample.h
+OBJECTS= ContextBase.o ContextIntersect.o ContextMap.o ContextSample.o
 _EXT_OBJECTS=ParseTools.o QuickString.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -31,6 +31,9 @@ $(BUILT_OBJECTS): $(SOURCES)
 
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/ContextBase.o $(OBJ_DIR)/ContextIntersect.o $(OBJ_DIR)/ContextSample.o
+	@rm -f $(OBJ_DIR)/ContextBase.o \
+	       $(OBJ_DIR)/ContextIntersect.o \
+	       $(OBJ_DIR)/ContextMap.o \
+	       $(OBJ_DIR)/ContextSample.o
 
 .PHONY: clean
\ No newline at end of file

src/utils/FileRecordTools/RecordOutputMgr.cpp

@@ -117,6 +117,18 @@ void RecordOutputMgr::printRecord(const Record *record)
 	printRecord(keyList);
 }
 
+void RecordOutputMgr::printRecord(const Record *record, const string value)
+{	
+	RecordKeyList keyList(record);
+	printRecord(keyList);
+	_outBuf.append(value.c_str());
+	newline();
+
+	if (needsFlush()) {
+		flush();
+	}
+}
+
 void RecordOutputMgr::printRecord(RecordKeyList &keyList) {
 	if (keyList.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
 		RecordKeyList blockList(keyList.getKey());
@@ -129,7 +141,6 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList) {
 		return;
 	}
     printRecord(keyList, NULL);
-
 }
 
 void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockList)
@@ -192,6 +203,12 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
 		}
 		_currBlockList = NULL;
 		return;
+	} else if (_context->getProgram() == ContextBase::MAP) {
+		if (!printKeyAndTerminate(keyList)) {
+			tab();
+		}
+		_currBlockList = NULL;
+		return;
 	}
 }
 

src/utils/FileRecordTools/RecordOutputMgr.h

@@ -27,6 +27,8 @@ public:
 //	void printHeader(const string &);
 	void printRecord(const Record *record);
 	void printRecord(RecordKeyList &keyList);
+	// Added by ARQ
+	void printRecord(const Record *record, const string value);
 
 private:
 	typedef enum { NOT_BAM, BAM_AS_BAM, BAM_AS_BED} printBamType;