jpayne@69: #-- Imported variables from top level makefile
jpayne@69: # BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
jpayne@69: 
jpayne@69: ifndef BIN_DIR
jpayne@69: BIN_DIR := $(CURDIR)
jpayne@69: endif
jpayne@69: ifndef AUX_BIN_DIR
jpayne@69: AUX_BIN_DIR := $(CURDIR)
jpayne@69: endif
jpayne@69: 
jpayne@69: OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
jpayne@69: BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
jpayne@69:            chmod 755 $(BIN_DIR)/$@
jpayne@69: AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
jpayne@69:            chmod 755 $(AUX_BIN_DIR)/$@
jpayne@69: VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
jpayne@69: 
jpayne@69: ALL := annotate combineMUMs delta-filter gaps mgaps \
jpayne@69:      postnuc postpro prenuc prepro repeat-match \
jpayne@69:      show-aligns show-coords show-tiling show-snps \
jpayne@69:      show-diff
jpayne@69: 
jpayne@69: 
jpayne@69: #-- PHONY rules --#
jpayne@69: .PHONY: all clean
jpayne@69: 
jpayne@69: 
jpayne@69: all: $(ALL)
jpayne@69: 
jpayne@69: 
jpayne@69: clean:
jpayne@69: 	rm -f *.o *~
jpayne@69: 	cd $(BIN_DIR); rm -f $(ALL)
jpayne@69: 	cd $(AUX_BIN_DIR); rm -f $(ALL)
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: #-- not so PHONY rules --#
jpayne@69: delta.o: delta.cc delta.hh
jpayne@69: 	$(OBJ_RULE)
jpayne@69: 
jpayne@69: tigrinc.o: tigrinc.cc tigrinc.hh
jpayne@69: 	$(OBJ_RULE)
jpayne@69: 
jpayne@69: sw_align.o: sw_align.cc sw_align.hh tigrinc.hh
jpayne@69: 	$(OBJ_RULE)
jpayne@69: 
jpayne@69: translate.o: translate.cc translate.hh
jpayne@69: 	$(OBJ_RULE)
jpayne@69: 
jpayne@69: 
jpayne@69: annotate: annotate.cc tigrinc.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: combineMUMs: combineMUMs.cc tigrinc.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: delta-filter: delta-filter.cc tigrinc.o delta.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: gaps: gaps.cc tigrinc.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: mgaps: mgaps.cc tigrinc.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: postnuc: postnuc.cc tigrinc.o sw_align.o
jpayne@69: 	$(AUX_BIN_RULE)
jpayne@69: 
jpayne@69: postpro: postpro.cc tigrinc.o sw_align.o translate.o
jpayne@69: 	$(AUX_BIN_RULE)
jpayne@69: 
jpayne@69: prenuc: prenuc.cc tigrinc.o
jpayne@69: 	$(AUX_BIN_RULE)
jpayne@69: 
jpayne@69: prepro: prepro.cc tigrinc.o translate.o
jpayne@69: 	$(AUX_BIN_RULE)
jpayne@69: 
jpayne@69: repeat-match: repeat-match.cc tigrinc.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: show-aligns: show-aligns.cc tigrinc.o translate.o delta.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: show-coords: show-coords.cc tigrinc.o delta.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: show-tiling: show-tiling.cc tigrinc.o delta.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: show-snps: show-snps.cc tigrinc.o translate.o delta.o
jpayne@69: 	$(BIN_RULE)
jpayne@69: 
jpayne@69: show-diff: show-diff.cc tigrinc.o delta.o
jpayne@69: 	$(BIN_RULE)