Merge branch 'master' of https://github.com/arq5x/bedtools2

Makefile

@@ -24,6 +24,8 @@ export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 export LIBS		= -lz
 export BT_ROOT  = src/utils/BamTools/
 
+prefix = /usr/local
+
 SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/bamToBed \
 		  $(SRC_DIR)/bamToFastq \
@@ -107,6 +109,12 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
 
 .PHONY: all
 
+install: all
+	mkdir -p $(DESTDIR)$(prefix)/bin
+	for file in bin/* ; do \
+		cp -f $$file $(DESTDIR)$(prefix)/bin; \
+	done
+
 print_banner:
 	@echo "Building BEDTools:"
 	@echo "========================================================="

src/pairToPair/pairToPair.cpp

@@ -136,7 +136,7 @@ void PairToPair::FindOverlaps(const BEDPE &a) {
 bool PairToPair::FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
                                     const vector<MATE> &qualityHitsEnd2) {
 
-    map<unsigned int, vector<MATE>, less<int> > hitsMap;
+    map<unsigned int, vector<MATE>, less<unsigned int> > hitsMap;
 
     for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) {
         hitsMap[h->lineNum].push_back(*h);
@@ -174,7 +174,7 @@ bool PairToPair::FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityH
 void PairToPair::FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
                                     const vector<MATE> &qualityHitsEnd2) {
 
-    map<unsigned int, vector<MATE>, less<int> > hitsMap;
+    map<unsigned int, vector<MATE>, less<unsigned int> > hitsMap;
 
     for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) {
         hitsMap[h->lineNum].push_back(*h);