3 # Use 64-bit integers in a 64-bit environment.
4 # SIZE_FLAGS = -DMASSIVE_DATA_RLCSA
6 # Parallelism is supported by either libstdc++ Parallel Mode or MCSTL.
7 # PARALLEL_FLAGS = -DMULTITHREAD_SUPPORT -D_GLIBCXX_PARALLEL -fopenmp
8 # MCSTL_ROOT = /fs-3/d/jltsiren/suds/mcstl
9 # PARALLEL_FLAGS = -DMULTITHREAD_SUPPORT -I$(MCSTL_ROOT)/c++ -fopenmp
11 # Vectors using nibble codes instead of delta codes are faster, but they also
13 # VECTOR_FLAGS = -DUSE_NIBBLE_VECTORS
15 #CPPFLAGS = -Wall -g $(SIZE_FLAGS) $(PARALLEL_FLAGS) $(VECTOR_FLAGS)
16 CPPFLAGS = -Wall -O3 $(SIZE_FLAGS) $(PARALLEL_FLAGS) $(VECTOR_FLAGS)
17 OBJS = rlcsa.o rlcsa_builder.o sasamples.o lcpsamples.o bits/array.o bits/bitvector.o bits/deltavector.o bits/rlevector.o bits/nibblevector.o misc/parameters.o misc/utils.o qsufsort/qsufsort.o
19 VPATH = bits:misc:utils
26 ar rcs rlcsa.a $(OBJS)
29 g++ -MM *.cpp bits/*.cpp misc/*.cpp qsufsort/*.c utils/*.cpp > dependencies.mk
31 rlcsa_test: rlcsa_test.o rlcsa.a
32 $(CC) $(CPPFLAGS) -o rlcsa_test rlcsa_test.o rlcsa.a
34 lcp_test: lcp_test.o rlcsa.a
35 $(CC) $(CPPFLAGS) -o lcp_test lcp_test.o rlcsa.a
37 parallel_build: parallel_build.o rlcsa.a
38 $(CC) $(CPPFLAGS) -o parallel_build parallel_build.o rlcsa.a
40 build_rlcsa: build_rlcsa.o rlcsa.a
41 $(CC) $(CPPFLAGS) -o build_rlcsa build_rlcsa.o rlcsa.a
43 locate_test: locate_test.o rlcsa.a
44 $(CC) $(CPPFLAGS) -o locate_test locate_test.o rlcsa.a
46 display_test: display_test.o rlcsa.a
47 $(CC) $(CPPFLAGS) -o display_test display_test.o rlcsa.a
49 read_bwt: read_bwt.o rlcsa.a
50 $(CC) $(CPPFLAGS) -o read_bwt read_bwt.o rlcsa.a
52 extract_sequence: extract_sequence.o rlcsa.a
53 $(CC) $(CPPFLAGS) -o extract_sequence extract_sequence.o rlcsa.a
55 rlcsa_grep: rlcsa_grep.o rlcsa.a
56 $(CC) $(CPPFLAGS) -o rlcsa_grep rlcsa_grep.o rlcsa.a
58 build_plcp: build_plcp.o rlcsa.a
59 $(CC) $(CPPFLAGS) -o build_plcp build_plcp.o rlcsa.a
61 sample_lcp: sample_lcp.o rlcsa.a
62 $(CC) $(CPPFLAGS) -o sample_lcp sample_lcp.o rlcsa.a
64 extract_text: extract_text.o
65 $(CC) $(CPPFLAGS) -o utils/extract_text extract_text.o
67 convert_patterns: convert_patterns.o
68 $(CC) $(CPPFLAGS) -o utils/convert_patterns convert_patterns.o misc/utils.o
70 split_text: split_text.o
71 $(CC) $(CPPFLAGS) -o utils/split_text split_text.o misc/utils.o
73 genpatterns: genpatterns.c
74 gcc -O3 -Wall -o utils/genpatterns utils/genpatterns.c
77 rm -f rlcsa.a rlcsa_test lcp_test parallel_build
78 rm -f build_rlcsa locate_test display_test read_bwt extract_sequence rlcsa_grep build_plcp sample_lcp
79 rm -f utils/extract_text utils/convert_patterns utils/split_text
80 rm -f *.o bits/*.o misc/*.o qsufsort/*.o utils/*.o
84 mkdir rlcsa/bits rlcsa/misc rlcsa/qsufsort rlcsa/utils
85 cp LICENSE Makefile README dependencies.mk *.cpp *.h rlcsa
86 cp bits/*.cpp bits/*.h rlcsa/bits
87 cp misc/*.cpp misc/*.h rlcsa/misc
88 cp qsufsort/*.c qsufsort/*.h rlcsa/qsufsort
89 cp utils/*.cpp utils/*.py rlcsa/utils
90 tar cfz rlcsa.tgz rlcsa
94 include dependencies.mk