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174 lines
5.7 KiB
174 lines
5.7 KiB
--- a/src/Makefile
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+++ b/src/Makefile
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@@ -52,15 +52,13 @@
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WINMAKE=mingw32-make
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LDLIBS = -lm
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-AR = ar
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-CC = gcc
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-CPP = g++
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-O_OPTS = -O2
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-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__
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-P_DEFINES =
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-
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-CFLAGS = $(CC_OPTS) $(O_OPTS)
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-LDFLAGS = -g
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+O_OPTS ?=
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+CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__
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+P_DEFINES ?=
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+
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+CFLAGS += $(CC_OPTS) $(O_OPTS)
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+CXXFLAGS += $(CC_OPTS) $(O_OPTS)
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+LDFLAGS +=
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# Note, for profiling, use
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# make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
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@@ -92,7 +90,6 @@
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LIBPRIMER3_DYN = libprimer3.so.1.0.0
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LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM)
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DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
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-RANLIB = ranlib
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PRIMER_OBJECTS1=primer3_boulder_main.o\
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format_output.o\
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@@ -119,93 +116,89 @@
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ifeq ($(TESTOPTS),--windows)
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cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS)
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else
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- cd ../test/; make clean
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+ cd ../test/ && $(MAKE) clean
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endif
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$(LIBOLIGOTM): oligotm.o
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- $(AR) rv $@ oligotm.o
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- $(RANLIB) $@
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+ $(AR) rcs $@ oligotm.o
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$(LIBOLIGOTM_LIB): oligotm.o
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- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
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+ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
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$(LIBDPAL): dpal_primer.o
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- $(AR) rv $@ dpal_primer.o
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- $(RANLIB) $@
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+ $(AR) rcs $@ dpal_primer.o
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$(LIBDPAL_DYN): dpal_primer.o
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- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
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+ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
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$(LIBTHAL): thal_primer.o
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- $(AR) rv $@ thal_primer.o
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- $(RANLIB) $@
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+ $(AR) rcs $@ thal_primer.o
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$(LIBTHAL_DYN): thal_primer.o
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- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
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+ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
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$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
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- $(AR) rv $@ libprimer3.o p3_seq_lib.o
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- $(RANLIB) $@
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+ $(AR) rcs $@ libprimer3.o p3_seq_lib.o
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$(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
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- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
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+ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
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$(PRIMER_EXE): $(PRIMER_OBJECTS)
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- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
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+ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
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libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
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- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
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+ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
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$(NTDPAL_EXE): ntdpal_main.o dpal.o
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- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
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+ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
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$(NTTHAL_EXE): thal_main.o thal.o
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- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
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+ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
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$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
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- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
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$(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
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- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
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+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
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read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h
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- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
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+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
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print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
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- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
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+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
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dpal.o: dpal.c dpal.h
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- $(CPP) -c $(CFLAGS) -o $@ dpal.c
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+ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c
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# We use '-ffloat-store' on windows to prevent undesirable
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# precision which may lead to differences in floating point results.
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thal.o: thal.c thal.h
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- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
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+ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
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p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
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- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
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+ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
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dpal_primer.o: dpal.c dpal.h
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- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
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+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
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thal_primer.o: thal.c thal.h
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- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
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+ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
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format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
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- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
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+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
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ntdpal_main.o: ntdpal_main.c dpal.h
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- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
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+ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
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thal_main.o: thal_main.c thal.h
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- $(CPP) -c $(CFLAGS) -o $@ thal_main.c
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+ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
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# We use CC_OPTS above rather than CFLAGS because
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# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
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oligotm.o: oligotm.c oligotm.h
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primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
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- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
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+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
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primer_test: test
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@@ -213,7 +206,7 @@
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ifeq ($(TESTOPTS),--windows)
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cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS)
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else
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- cd ../test; make test
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+ cd ../test && $(MAKE) test
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endif
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# ======================================================================
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--- a/test/Makefile
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+++ b/test/Makefile
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@@ -86,7 +86,7 @@
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ifeq ($(TESTOPTS),--windows)
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cd ..\src & $(WINMAKE)
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else
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- cd ../src; make
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+ cd ../src && $(MAKE)
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endif
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clean:
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