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path: root/quake-0.3.1-makefile.patch
blob: 80878cb0fd2dee5ab9e142bf22c5a2987a4f2551 (plain)
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diff -rup old/src/Makefile new/src/Makefile
--- old/src/Makefile	2012-04-03 12:12:24.000000000 -0400
+++ new/src/Makefile	2012-06-14 23:46:18.330640119 -0400
@@ -1,8 +1,10 @@
-CC=g++
-CFLAGS=-O3 -fopenmp -I/opt/local/var/macports/software/boost/1.46.1_0/opt/local/include -I.
-LDFLAGS=-L. -lgzstream -lz
+CXX      := g++
+CXXFLAGS := $(CXXFLAGS) -fopenmp -I.
+LDFLAGS  := -L. -lgzstream -lz
 #INCLUDEDIR=
-EXE_FILES = correct count-kmers count-qmers count_qmers reduce-kmers reduce-qmers trim build_bithash correct_stats
+EXE_FILES := correct count-kmers count-qmers \
+		count_qmers reduce-kmers reduce-qmers \
+		trim build_bithash correct_stats
 .PHONY: all clean
 
 all: $(EXE_FILES)
@@ -11,49 +13,49 @@ clean:
 	-rm $(EXE_FILES) *.o
 
 correct: correct.cpp Read.o bithash.o edit.o libgzstream.a
-	$(CC) $(CFLAGS) correct.cpp Read.o bithash.o edit.o -o correct $(LDFLAGS)
+	$(CXX) $(CXXFLAGS) correct.cpp Read.o bithash.o edit.o -o correct $(LDFLAGS)
 
 count-kmers: count-kmers.cpp count.o
-	$(CC) $(CFLAGS) count-kmers.cpp count.o -o count-kmers
+	$(CXX) $(CXXFLAGS) count-kmers.cpp count.o -o count-kmers
 
 count-qmers: count-qmers.cpp count.o
-	$(CC) $(CFLAGS) count-qmers.cpp count.o -o count-qmers
+	$(CXX) $(CXXFLAGS) count-qmers.cpp count.o -o count-qmers
 
 count_qmers: count_qmers.cpp count.o qmer_hash.o
-	$(CC) $(CFLAGS) -o count_qmers count_qmers.cpp count.o qmer_hash.o
+	$(CXX) $(CXXFLAGS) -o count_qmers count_qmers.cpp count.o qmer_hash.o
 
 qmer_hash.o: qmer_hash.cpp qmer_hash.h
-	$(CC) $(CFLAGS) -c qmer_hash.cpp
+	$(CXX) $(CXXFLAGS) -c qmer_hash.cpp
 
 reduce-kmers: reduce-kmers.cpp
-	$(CC) $(CFLAGS) reduce-kmers.cpp -o reduce-kmers
+	$(CXX) $(CXXFLAGS) reduce-kmers.cpp -o reduce-kmers
 
 reduce-qmers: reduce-qmers.cpp
-	$(CC) $(CFLAGS) reduce-qmers.cpp -o reduce-qmers
+	$(CXX) $(CXXFLAGS) reduce-qmers.cpp -o reduce-qmers
 
 trim: trim.cpp Read.o bithash.o edit.o libgzstream.a
-	$(CC) $(CFLAGS) trim.cpp Read.o bithash.o edit.o -o trim $(LDFLAGS)
+	$(CXX) $(CXXFLAGS) trim.cpp Read.o bithash.o edit.o -o trim $(LDFLAGS)
 
 build_bithash: build_bithash.cpp bithash.o
-	$(CC) $(CFLAGS) build_bithash.cpp bithash.o -o build_bithash
+	$(CXX) $(CXXFLAGS) build_bithash.cpp bithash.o -o build_bithash
 
 correct_stats: stats.cpp
-	$(CC) $(CFLAGS) stats.cpp -o correct_stats
+	$(CXX) $(CXXFLAGS) stats.cpp -o correct_stats
 
 Read.o: Read.cpp Read.h bithash.o
-	$(CC) $(CFLAGS) -c Read.cpp
+	$(CXX) $(CXXFLAGS) -c Read.cpp
 
 edit.o: edit.cpp edit.h
-	$(CC) $(CFLAGS) -c edit.cpp
+	$(CXX) $(CXXFLAGS) -c edit.cpp
 
 bithash.o: bithash.cpp bithash.h
-	$(CC) $(CFLAGS) -c bithash.cpp
+	$(CXX) $(CXXFLAGS) -c bithash.cpp
 
 count.o: count.cpp
-	$(CC) $(CFLAGS) -c count.cpp
+	$(CXX) $(CXXFLAGS) -c count.cpp
 
 gzstream.o: gzstream.C gzstream.h
-	$(CC) $(CFLAGS) -c -o gzstream.o gzstream.C
+	$(CXX) $(CXXFLAGS) -c -o gzstream.o gzstream.C
 
 libgzstream.a: gzstream.o
 	ar cr libgzstream.a gzstream.o