right, the actual spacing code.

src/spacingFile/Makefile

+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+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)/FileRecordTools/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ 			-I$(UTILITIES_DIR)/KeyListOps/ \
+          -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+            -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= spacingMain.cpp SpacingFile.cpp SpacingFile.h
+OBJECTS= spacingMain.o SpacingFile.o
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= spacing
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/sampleMain.o $(OBJ_DIR)/SpacingFile.o
+
+.PHONY: clean

src/spacingFile/SpacingFile.cpp

+/*
+ * SpacingFile.cpp
+ *
+ *  Created on: Nov 18, 2013
+ *      Author: nek3d
+ */
+
+#include "SpacingFile.h"
+#include "ContextSpacing.h"
+#include "FileRecordMgr.h"
+#include "RecordOutputMgr.h"
+
+
+SpacingFile::SpacingFile(ContextSpacing *context)
+:	_context(context),
+	_inputFile(NULL),
+	_outputMgr(NULL)
+{}
+
+SpacingFile::~SpacingFile() {
+
+}
+
+bool SpacingFile::getSpacing()
+{
+	//we're only operating on one file, so the idx is zero.
+	_inputFile =  _context->getFile(0);
+
+
+	_outputMgr = new RecordOutputMgr();
+	_outputMgr->init(_context);
+
+	Record *prev = NULL;
+	Record *curr = NULL;
+	QuickString distance;
+	while (!_inputFile->eof()) {
+
+		Record *curr = _inputFile->getNextRecord();
+		
+		// no more records
+		if (curr == NULL) {
+			continue;
+		}
+		// first record in file.
+		if (prev == NULL) {
+			distance.append(".");
+		}
+		// the meat of the file
+		else {
+			// current and previous records are on the same chromosome.
+			if (curr->getChrName() == prev->getChrName())
+			{
+				// do curr and prev overlap?
+				if (curr->sameChromIntersects(prev, false, false, 1E-9, false))
+					distance.append(0);
+				else
+					distance.append(curr->getStartPos() - prev->getEndPos());
+			}
+			// we have changed chromosomes
+			else if (curr->getChrName() != prev->getChrName())
+			{
+				distance.append(".");
+			}
+		}
+		// report distance between current and previous intervals
+		_outputMgr->printRecord(curr, distance);
+		// memory cleanup
+		_inputFile->deleteRecord(prev);
+		distance.clear();
+
+		// current become previous in prep for next record in file.
+		prev = curr;
+	}
+
+	// cleanup
+	delete _outputMgr;
+	_inputFile->close();
+	return true;
+}
+
+

src/spacingFile/SpacingFile.h

+/*
+ * SpacingFile.h
+ *
+ *  Created on: Nov 18, 2013
+ *      Author: nek3d
+ */
+
+#ifndef SPACINGFILE_H_
+#define SPACINGFILE_H_
+
+#include "ContextSpacing.h"
+#include "Record.h"
+#include <vector>
+
+using namespace std;
+
+class FileRecordMgr;
+class Context;
+class RecordOutputMgr;
+
+class SpacingFile {
+public:
+	SpacingFile(ContextSpacing *context);
+	~SpacingFile();
+	bool getSpacing();
+
+private:
+	ContextSpacing *_context;
+	FileRecordMgr *_inputFile;
+	RecordOutputMgr *_outputMgr;
+
+
+};
+
+#endif /* SPACINGFILE_H_ */