diff --git a/Makefile b/Makefile
index e7b741ab8e5464b0bbb33bcba62e66fda56eb9fd..d61800288ed348916f91fa143c665f5303bd7b06 100755
--- a/Makefile
+++ b/Makefile
@@ -21,23 +21,27 @@ export CXX ?= g++
 # define our source subdirectories
 SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/peIntersectBed
 
-UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
+UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities
+
 all:
 
 	@echo "Building BEDTools:"
 	@echo "========================================================="
-	@for dir in $(SUBDIRS); do \
+	
+	@for dir in $(UTIL_SUBDIRS); do \
 		echo "- Building in $$dir"; \
 		$(MAKE) --no-print-directory -C $$dir; \
 		echo ""; \
 	done
 
-	@for dir in $(UTIL_SUBDIRS); do \
+	@for dir in $(SUBDIRS); do \
 		echo "- Building in $$dir"; \
 		$(MAKE) --no-print-directory -C $$dir; \
 		echo ""; \
 	done
 
+
+
 .PHONY: all
 
 clean:
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 36424f979729f495a8e41a1ebf15e0bf07b85726..2d9842ec848426c8eee531eae3f90230a55f34d6 100755
Binary files a/bin/genomeCoverageBed and b/bin/genomeCoverageBed differ
diff --git a/obj/genomeCoverageBed.o b/obj/genomeCoverageBed.o
index a17a58acf05989b004bffdd3e3e8ee54d36406e1..980382d644a13ca8af1d6fa624c2a82e66f9a4d7 100644
Binary files a/obj/genomeCoverageBed.o and b/obj/genomeCoverageBed.o differ
diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
index eccf14ad276152df0d8bbb5b84ac921a0835bc62..45bb001699b15eeb5c67be2d28f54d226b9bba21 100644
Binary files a/obj/genomeCoverageMain.o and b/obj/genomeCoverageMain.o differ
diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile
index 3b703f2d9b7912ae7c6b4f2c6609da732474efb3..06e88fba07f018be447ff66dbf7d22226b7f0806 100755
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -38,8 +38,7 @@ $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-
-		
+	
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
diff --git a/src/genomeCoverageBed/genomeCoverageBed.cpp b/src/genomeCoverageBed/genomeCoverageBed.cpp
index 8e3d899abb91127ef3f070fae99929778774f612..eeaccb819e854430e2084e27bb36576bf0e2da33 100755
--- a/src/genomeCoverageBed/genomeCoverageBed.cpp
+++ b/src/genomeCoverageBed/genomeCoverageBed.cpp
@@ -117,6 +117,9 @@ void BedCoverage::CoverageBeds() {
 						depth += this->chromCov[chrom][pos];
 						this->chromCov[chrom][pos] = depth;
 					}
+					else {
+						this->chromCov[chrom][pos] = depth;
+					}
 					
 					// report the depth for this position.
 					cout << chrom << "\t" << pos+1 << "\t" << this->chromCov[chrom][pos] << endl; 
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index b64cbacf80a620f1a06d22233c2738fa56b5b313..d31d338c7bfa4d9801cdea9f38e276917b379b80 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -62,10 +62,10 @@ int main(int argc, char* argv[]) {
 			eachBase = true;
 			i++;
 		}
-		else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
-			startSites = true;
-			i++;
-		}
+		//else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+		//	startSites = true;
+		//	i++;
+		//}
 		else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
 			max = atoi(argv[i + 1]);
 			i++;
@@ -108,7 +108,7 @@ void ShowHelp(void) {
 	
 	cerr << "OPTIONS: " << endl;
 	cerr << "\t" << "-d\t\t\t"            	<< "Report the depth at each genome position." << endl << "\t\t\t\tDefault behavior is to report a histogram." << endl << endl;
-	cerr << "\t" << "-s \t\t\t"             << "Report depth based on start sites." << endl << endl;
+	//	cerr << "\t" << "-s \t\t\t"             << "Report depth based on start sites." << endl << endl;
 	cerr << "\t" << "-max\t\t\t"            << "Combine all positions with a depth > max into a single bin in the histogram." << endl << endl;
 	cerr << "NOTES: " << endl;
 	cerr << "\tThe genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
diff --git a/src/intersectBed/13.out b/src/intersectBed/13.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/13.out
@@ -0,0 +1,39585 @@
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diff --git a/src/intersectBed/17.out b/src/intersectBed/17.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/17.out
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diff --git a/src/intersectBed/chr1_snp129.bed b/src/intersectBed/chr1_snp129.bed
new file mode 100644
index 0000000000000000000000000000000000000000..97fe24a97322bd34f64c612994dd90747aa734a2
--- /dev/null
+++ b/src/intersectBed/chr1_snp129.bed
@@ -0,0 +1,36707 @@
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diff --git a/src/intersectBed/new.out b/src/intersectBed/new.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/new.out
@@ -0,0 +1,39585 @@
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+chr1	4947801	4947805	rs33911980	0	+
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+chr1	4957731	4957732	rs12134477	0	+
+chr1	4958984	4958985	rs12354399	0	+
+chr1	4959008	4959009	rs9727498	0	+
+chr1	4960335	4960336	rs9286972	0	+
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+chr1	4960834	4960835	rs10157316	0	+
+chr1	4961076	4961077	rs1380469	0	+
+chr1	4961366	4961391	rs59532263	0	+
+chr1	4961378	4961379	rs59532263	0	+
+chr1	4961378	4961379	rs10158288	0	+
+chr1	4961378	4961379	rs10158288	0	+
+chr1	4961538	4961539	rs12735198	0	+
+chr1	4961548	4961549	rs12091364	0	+
+chr1	4962035	4962060	rs57626559	0	+
+chr1	4962047	4962048	rs57626559	0	+
+chr1	4962047	4962048	rs11808607	0	+
+chr1	4962047	4962048	rs11808607	0	+
+chr1	4963140	4963165	rs60782198	0	+
+chr1	4963152	4963153	rs60782198	0	+
+chr1	4963152	4963153	rs10915307	0	+
+chr1	4963152	4963153	rs10915307	0	+
+chr1	4963979	4963980	rs34723678	0	+
+chr1	4964052	4964077	rs58487803	0	+
+chr1	4964064	4964065	rs58487803	0	+
+chr1	4964064	4964065	rs10737393	0	+
+chr1	4964064	4964065	rs10737393	0	+
+chr1	4964295	4964296	rs11588948	0	+
+chr1	4964531	4964532	rs28667637	0	+
+chr1	4964975	4964976	rs12027167	0	+
+chr1	4964980	4964981	rs58040193	0	+
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+chr1	4965202	4965203	rs59467151	0	+
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+chr1	4965448	4965449	rs10915308	0	+
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+chr1	4965697	4965722	rs60029593	0	+
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+chr1	4968069	4968070	rs10915310	0	+
+chr1	4968092	4968117	rs56873828	0	+
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+chr1	4968104	4968105	rs10799151	0	+
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+chr1	4969530	4969538	rs60284801	0	+
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+chr1	4997394	4997395	rs7538599	0	+
+chr1	4997880	4997881	rs1157959	0	-
+chr1	4998053	4998054	rs11801677	0	+
+chr1	4998122	4998123	rs12121943	0	+
+chr1	4998179	4998180	rs12118656	0	+
+chr1	4998332	4998333	rs61401760	0	+
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diff --git a/src/peIntersectBed/peIntersectBed.cpp b/src/peIntersectBed/peIntersectBed.cpp
index d4d6b15472c3a7b53e2e685f518aa1e92a495d52..4228f1a54837b7dea1694a7f258c5dddb7963d5c 100755
--- a/src/peIntersectBed/peIntersectBed.cpp
+++ b/src/peIntersectBed/peIntersectBed.cpp
@@ -179,6 +179,7 @@ void BedIntersectPE::FindSpanningOverlaps(BEDPE &a, vector<BED> &hits, string &t
 		int s = max(spanStart, h->start);
 		int e = min(spanEnd, h->end);
 
+		// overlap if s < e
 		if (s < e) {
 			
 			// is there enough overlap (default ~ 1bp)
diff --git a/src/peIntersectBed/peIntersectMain.cpp b/src/peIntersectBed/peIntersectMain.cpp
index 93bdbdb823c70cd0a373687c75d209709842ec6a..1d46d937929d572d1db7c315e7b7ba061122a3cd 100755
--- a/src/peIntersectBed/peIntersectMain.cpp
+++ b/src/peIntersectBed/peIntersectMain.cpp
@@ -25,6 +25,7 @@ int main(int argc, char* argv[]) {
 	float overlapFraction = 1E-9;
 	string searchType = "either";
 
+	// flags to track parameters
 	bool haveBedA = false;
 	bool haveBedB = false;
 	bool haveSearchType = false;
@@ -81,6 +82,7 @@ int main(int argc, char* argv[]) {
 		}		
 	}
 
+
 	// make sure we have both input files
 	if (!haveBedA || !haveBedB) {
 		cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
diff --git a/src/utils/bedFile/Makefile b/src/utils/bedFile/Makefile
index 900d6a422ae15f70bcdda37efb5857199ef24e11..41a166865a358cbe0e3d07fc8bdd01620d8ad548 100755
--- a/src/utils/bedFile/Makefile
+++ b/src/utils/bedFile/Makefile
@@ -23,7 +23,7 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(INCLUDES)
+	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index fbdf44f38ba03c0daaa8bdb57e9620a2d11aa82e..db1c7fa8582ae2f7bb1a8a2552b3530d37713425 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -16,19 +16,23 @@
 
 static int binOffsetsExtended[] =
 	{4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0};
-//static int binOffsets[] = {512+64+8+1, 64+8+1, 8+1, 1, 0};
-#define _binFirstShift 17/* How much to shift to get to finest bin. */
-#define _binNextShift 3/* How much to shift to get to next larger bin. */
+
+	
+#define _binFirstShift 17	/* How much to shift to get to finest bin. */
+#define _binNextShift 3		/* How much to shift to get to next larger bin. */
 
 
+// return the amount of overlap between two features.  Negative if none.
 int overlaps(const int aS, const int aE, const int bS, const int bE) {
 	return min(aE, bE) - max(aS, bS);
 }
 
+
 bool leftOf(const int a, const int b) {
 	return (a < b);
 }
 
+// return the lesser of two values.
 int min(const int a, int b) {
 	if (a <= b) {
 		return a;
@@ -38,6 +42,7 @@ int min(const int a, int b) {
 	}
 }
 
+// return the greater of two values.
 int max(const int a, int b) {
 	if (a >= b) {
 		return a;
@@ -47,9 +52,6 @@ int max(const int a, int b) {
 	}
 }
 
-//************************************************
-// Exception checking
-//************************************************
 
 static int getBin(int start, int end)
 /* 
@@ -64,14 +66,15 @@ static int getBin(int start, int end)
 	int startBin = start, endBin = end-1, i;
 	startBin >>= _binFirstShift;
 	endBin >>= _binFirstShift;
-	for (i=0; i<6; ++i)
-	{
+	
+	for (i=0; i<6; ++i) {
 		if (startBin == endBin) {
 			return binOffsetsExtended[i] + startBin;
 		}
 		startBin >>= _binNextShift;
 		endBin >>= _binNextShift;
 	}
+	
 	cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl;
 	return 0;
 }
@@ -129,31 +132,27 @@ bool byChromThenStart(BED const & a, BED const & b){
 	return false;
 };
 
-void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits)
-/* 
+
+/*
 	NOTE: Taken ~verbatim from kent source.
 	Return a list of all items in binKeeper that intersect range.
 	
-	* Free this list with slFreeList. */
-	
-{
+	Free this list with slFreeList.
+*/
+void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits) {
+
 	int startBin, endBin;
 	int i,j;
 
 	startBin = (start>>_binFirstShift);
 	endBin = ((end-1)>>_binFirstShift);
-	for (i=0; i<6; ++i)
-	{
+	for (i=0; i<6; ++i) {
 		int offset = binOffsetsExtended[i];
 
-		for (j=(startBin+offset); j<=(endBin+offset); ++j)  
-		{
+		for (j = (startBin+offset); j <= (endBin+offset); ++j)  {
 			for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
-				{
-					if (overlaps(el->start, el->end, start, end) > 0)
-					{
-						hits.push_back(*el);
-					}
+				if (overlaps(el->start, el->end, start, end) > 0) {
+					hits.push_back(*el);
 				}
 			}
 		}
@@ -163,27 +162,19 @@ void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const in
 }
 
 
-void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end)
-/* Return a list of all items in binKeeper that intersect range.
-	* Free this list with slFreeList. */
-{
+void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end) {
 	int startBin, endBin;
 	int i,j;
 
 	startBin = (start>>_binFirstShift);
 	endBin = ((end-1)>>_binFirstShift);
-	for (i=0; i<6; ++i)
-	{
+	for (i=0; i<6; ++i) {
 		int offset = binOffsetsExtended[i];
 
-		for (j=(startBin+offset); j<=(endBin+offset); ++j)  
-		{
+		for (j = (startBin+offset); j <= (endBin+offset); ++j) {
 			for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
-				{
-					if (overlaps(el->start, el->end, start, end) > 0)
-					{
-						el->count++;
-					}
+				if (overlaps(el->start, el->end, start, end) > 0) {
+					el->count++;
 				}
 			}
 		}
@@ -350,6 +341,7 @@ void BedFile::loadBedFileIntoMap() {
 	}
 }
 
+
 void BedFile::loadBedFileIntoMapNoBin() {
 
 	string bedLine;