diff --git a/src/closestBed/Makefile b/src/closestBed/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..abe0eee0a0d1a612afe17c1310a535b16a0031a5
--- /dev/null
+++ b/src/closestBed/Makefile
@@ -0,0 +1,44 @@
+CXX = g++
+CXXFLAGS = -O3
+LDFLAGS =
+
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= closestMain.cpp closestBed.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=bedFile.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= closestBed
+LIBS=
+
+all: $(PROGRAM)
+
+.PHONY: all
+
+$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ @echo " * linking $(PROGRAM)"
+ @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
new file mode 100755
index 0000000000000000000000000000000000000000..34725f56806887050db57f59f942cdb0edc1fff1
--- /dev/null
+++ b/src/closestBed/closestBed.cpp
@@ -0,0 +1,261 @@
+//
+// closestBed.cpp
+// BEDTools
+//
+// Created by Aaron Quinlan Spring 2009.
+// Copyright 2009 Aaron Quinlan. All rights reserved.
+//
+// Summary: Looks for the closest features in two BED files.
+//
+
+/*
+ Includes
+*/
+#include "closestBed.h"
+
+const int MAXSLOP = 256000000; // 2*MAXSLOP = 512 megabases.
+ // We don't want to keep looking if we
+ // can't find a nearby feature within 512 Mb.
+const int SLOPGROWTH = 2048000;
+
+
+/*
+ Constructor
+*/
+BedClosest::BedClosest(string &bedAFile, string &bedBFile) {
+
+ this->bedAFile = bedAFile;
+ this->bedBFile = bedBFile;
+
+ this->bedA = new BedFile(bedAFile);
+ this->bedB = new BedFile(bedBFile);
+}
+
+/*
+ Destructor
+*/
+BedClosest::~BedClosest(void) {
+}
+
+
+
+/*
+ reportA
+
+ Writes the _original_ BED entry for A.
+ Works for BED3 - BED6.
+*/
+void BedClosest::reportA(const BED &a) {
+
+ if (bedA->bedType == 3) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end;
+ }
+ else if (bedA->bedType == 4) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name;
+ }
+ else if (bedA->bedType == 5) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name << "\t" << a.score;
+ }
+ else if (bedA->bedType == 6) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name << "\t" << a.score << "\t" << a.strand;
+ }
+}
+
+
+
+/*
+ reportB
+
+ Writes the _original_ BED entry for B.
+ Works for BED3 - BED6.
+*/
+void BedClosest::reportB(const BED &b) {
+ if (bedB->bedType == 3) {
+ cout << b.chrom << "\t" << b.start << "\t" << b.end;
+ }
+ else if (bedB->bedType == 4) {
+ cout << b.chrom << "\t" << b.start << "\t" << b.end << "\t"
+ << b.name;
+ }
+ else if (bedB->bedType == 5) {
+ cout << b.chrom << "\t" << b.start << "\t" << b.end << "\t"
+ << b.name << "\t" << b.score;
+ }
+ else if (bedB->bedType == 6) {
+ cout << b.chrom << "\t" << b.start << "\t" << b.end << "\t"
+ << b.name << "\t" << b.score << "\t" << b.strand;
+ }
+}
+
+
+
+
+/*
+ reportNullB
+
+ Writes a NULL B entry for cases where no closest BED was found
+ Works for BED3 - BED6.
+*/
+void BedClosest::reportNullB() {
+ if (bedB->bedType == 3) {
+ cout << "none" << "\t" << "-1" << "\t" << "-1";
+ }
+ else if (bedB->bedType == 4) {
+ cout << "none" << "\t" << "-1" << "\t" << "-1" << "\t"
+ << "-1";
+ }
+ else if (bedB->bedType == 5) {
+ cout << "none" << "\t" << "-1" << "\t" << "-1" << "\t"
+ << "-1" << "\t" << "-1";
+ }
+ else if (bedB->bedType == 6) {
+ cout << "none" << "\t" << "-1" << "\t" << "-1" << "\t"
+ << "-1" << "\t" << "-1" << "\t" << "-1";
+ }
+}
+
+
+
+
+void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
+
+ int slop = SLOPGROWTH; // start out just looking for overlaps
+ // within the current bin (~128Kb)
+
+ // update the current feature's start and end
+
+ int aFudgeStart = 0;
+ int aFudgeEnd;
+ int numOverlaps = 0;
+ BED closestB;
+ float maxOverlap = 0;
+ int minDistance = 999999999;
+
+
+ if(bedB->bedMap.find(a.chrom) != bedB->bedMap.end()) {
+
+ while ((numOverlaps == 0) && (slop <= MAXSLOP)) {
+
+ if ((a.start - slop) > 0) {
+ aFudgeStart = a.start - slop;
+ }
+ else {
+ aFudgeEnd;
+ }
+ aFudgeEnd = a.end + slop;
+
+ bedB->binKeeperFind(bedB->bedMap[a.chrom], aFudgeStart, aFudgeEnd, hits);
+
+ for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
+
+ numOverlaps++;
+
+ // do the actual features overlap?
+ int s = max(a.start, h->start);
+ int e = min(a.end, h->end);
+
+ if (s < e) {
+
+ // is there enough overlap (default ~ 1bp)
+ float overlap = (float)(e-s) / (float)(a.end - a.start);
+
+ if ( overlap > 0 ) {
+
+ // is this hit the closest?
+ if (overlap > maxOverlap) {
+ closestB = *h;
+ maxOverlap = overlap;
+ }
+ }
+ }
+ else if (h->end < a.start){
+ if ((a.start - h->end) < minDistance) {
+ closestB = *h;
+ minDistance = a.start - h->end;
+ }
+ }
+ else {
+ if ((h->start - a.end) < minDistance) {
+ closestB = *h;
+ minDistance = h->start - a.end;
+ }
+ }
+
+ }
+ slop += SLOPGROWTH; // if there were no overlaps,
+ // we'll widen the range by 64Kb in each direction
+ }
+ }
+ else {
+ reportA(a);
+ cout << "\t";
+ reportNullB();
+ cout << "\n";
+ }
+
+ if (numOverlaps > 0) {
+ reportA(a);
+ cout << "\t";
+ reportB(closestB);
+ cout << "\n";
+ }
+}
+
+
+void BedClosest::ClosestBed() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bedB->loadBedFileIntoMap();
+
+
+ string bedLine;
+ BED bedEntry;
+ int lineNum = 0;
+
+ // open the BED file for reading
+ if (bedA->bedFile != "stdin") {
+
+ ifstream bed(bedA->bedFile.c_str(), ios::in);
+ if ( !bed ) {
+ cerr << "Error: The requested bed file (" <<bedA->bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+
+ BED a;
+ while (getline(bed, bedLine)) {
+
+ vector<string> bedFields;
+ Tokenize(bedLine,bedFields);
+
+ lineNum++;
+ if (bedA->parseBedLine(a, bedFields, lineNum)) {
+ vector<BED> hits;
+ FindWindowOverlaps(a, hits);
+ }
+ }
+ }
+ // "A" is being passed via STDIN.
+ else {
+
+ BED a;
+ while (getline(cin, bedLine)) {
+
+ vector<string> bedFields;
+ Tokenize(bedLine,bedFields);
+
+ lineNum++;
+ if (bedA->parseBedLine(a, bedFields, lineNum)) {
+
+ vector<BED> hits;
+ FindWindowOverlaps(a, hits);
+ }
+ }
+ }
+}
+// END ClosestBed
+
+
diff --git a/src/closestBed/closestBed.h b/src/closestBed/closestBed.h
new file mode 100755
index 0000000000000000000000000000000000000000..641f0df3c8008e722261a04953e5250f9b6473f3
--- /dev/null
+++ b/src/closestBed/closestBed.h
@@ -0,0 +1,49 @@
+#ifndef CLOSESTBED_H
+#define CLOSESTBED_H
+
+#include "bedFile.h"
+#include <vector>
+#include <map>
+#include <list>
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+
+//***********************************************
+// Typedefs
+//***********************************************
+typedef list<BED> bedList;
+
+
+//************************************************
+// Class methods and elements
+//************************************************
+class BedClosest {
+
+public:
+
+ // constructor
+ BedClosest(string &, string &);
+
+ // destructor
+ ~BedClosest(void);
+
+ void reportA(const BED &);
+ void reportB(const BED &);
+ void reportNullB();
+
+ void ClosestBed();
+ void FindWindowOverlaps(BED &, vector<BED> &);
+
+private:
+
+ string bedAFile;
+ string bedBFile;
+
+ // instance of a bed file class.
+ BedFile *bedA, *bedB;
+
+};
+#endif /* CLOSEST_H */
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d36dbfa08628025205313db85ab0358977caaeb4
--- /dev/null
+++ b/src/closestBed/closestMain.cpp
@@ -0,0 +1,99 @@
+#include "closestBed.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "closestBed"
+
+// define the version
+#define VERSION "1.1.0"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+// function declarations
+void ShowHelp(void);
+
+int main(int argc, char* argv[]) {
+
+ // our configuration variables
+ bool showHelp = false;
+
+ // input files
+ string bedAFile;
+ string bedBFile;
+
+ // input arguments
+ int slop = 0;
+
+ bool haveBedA = false;
+ bool haveBedB = 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) ShowHelp();
+
+ // 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)) {
+ haveBedA = true;
+ bedAFile = argv[i + 1];
+ i++;
+ }
+ else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
+ haveBedB = true;
+ bedBFile = argv[i + 1];
+ i++;
+ }
+ }
+
+ // make sure we have both input files
+ if (!haveBedA || !haveBedB) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+ showHelp = true;
+ }
+
+ if (!showHelp) {
+ BedClosest *bc = new BedClosest(bedAFile, bedBFile);
+ bc->ClosestBed();
+ return 0;
+ }
+ else {
+ ShowHelp();
+ }
+}
+
+void ShowHelp(void) {
+
+ cerr << "===============================================" << endl;
+ cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
+ cerr << " Hall Laboratory, University of Virginia" << endl;
+ cerr << "===============================================" << endl << endl;
+ cerr << "Description: For each feature in BED A, finds the closest feature (upstream or downstream) in BED B" << endl;
+
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+
+ cerr << "NOTES: " << endl;
+ cerr << "\t" << "-i stdin " << "allows closestBed to read BED A from stdin. E.g.: cat a.bed | closestBed -a stdin -b B.bed" << endl << endl;
+ cerr << "\t" << "Reports \"none\" for chrom and \"-1\" for all other fields when a feature is not found in B on the same chromosome as the feature in A. E.g. none -1 -1" << endl;
+
+ // end the program here
+ exit(1);
+
+}