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@@ -2,3 +2,5 @@ src/*.o | |
| .vscode/settings.json | ||
| .gitignore | ||
| v1.0.zip | ||
| *.gch | ||
| src/AlcoR | ||
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| #============================================================================# | ||
| # | ||
| # AlcoR 2023 IEETA/DETI, UNIVERSITY OF AVEIRO | ||
| # | ||
| #============================================================================# | ||
| BIN = . | ||
| CC = gcc | ||
| CPLP = | ||
| #----------------------------------------------------------------------------- | ||
| CFLAGS = -Wall -Ofast -march=native -mtune=native $(CPLP) | ||
| #----------------------------------------------------------------------------- | ||
| LIBS = -lm | ||
| DEPS = defs.h mem.h | ||
| ALCOR_DEPS = keys.h msg.h dna.h param.h common.h levels.h strings.h lr.h si.h ex.h vi.h | ||
| ALHABET_DEPS = common.h | ||
| CM_DEPS = dna.h msg.h common.h alphabet.h tolerant.h rand.h carray.h buffer.h pmodels.h chash.h | ||
| COMMON_DEPS = msg.h | ||
| DIST_DEPS = common.h alphabet.h | ||
| DNA_DEPS = common.h msg.h | ||
| EX_DEPS = dna.h msg.h buffer.h common.h strings.h param.h | ||
| KMER_DEPS = common.h dna.h | ||
| LEVELS_DEPS = msg.h | ||
| LR_DEPS = threads.h msg.h dna.h buffer.h levels.h param.h alphabet.h common.h cache.h positions.h pmodels.h strings.h cm.h | ||
| PAINT_DEPS = common.h msg.h | ||
| PARAM_DEPS = common.h msg.h dna.h strings.h keys.h alphabet.h | ||
| PMODELS_DEPS = math.h common.h | ||
| SI_DEPS = cm.h dna.h msg.h rand.h buffer.h common.h strings.h param.h | ||
| STRINGS_DEPS = msg.h | ||
| TOLERANT_DEPS = strings.h pmodels.h buffer.h | ||
| VI_DEPS = dna.h msg.h buffer.h common.h strings.h param.h paint.h | ||
| IF_DEPS = dna.h msg.h buffer.h common.h strings.h param.h | ||
| PROG = $(BIN)/AlcoR | ||
| OBJS = mem.o positions.o stats.o rand.o math.o buffer.o chash.o carray.o \ | ||
| cache.o filter.o keys.o msg.o strings.o common.o alphabet.o dist.o \ | ||
| dna.o kmer.o levels.o ex.o paint.o param.o pmodels.o tolerant.o if.o cm.o vi.o lr.o si.o | ||
| #----------------------------------------------------------------------------- | ||
|
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| all: progs | ||
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| progs: $(PROG) | ||
| $(BIN)/AlcoR: alcor.c $(DEPS) $(OBJS) | ||
| $(CC) $(CFLAGS) -o $(BIN)/AlcoR alcor.c $(OBJS) $(LIBS) | ||
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| alphabet.o: alphabet.c alphabet.h $(DEPS) $(ALHABET_DEPS) | ||
| $(CC) -c $(CFLAGS) alphabet.c | ||
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| buffer.o: buffer.c buffer.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) buffer.c | ||
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| cache.o: cache.c cache.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) cache.c | ||
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| carray.o: carray.c carray.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) carray.c | ||
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| chash.o: chash.c chash.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) chash.c | ||
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| cm.o: cm.c cm.h $(DEPS) $(CM_DEPS) | ||
| $(CC) -c $(CFLAGS) cm.c | ||
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| common.o: common.c common.h $(DEPS) $(COMMON_DEPS) | ||
| $(CC) -c $(CFLAGS) common.c | ||
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| defs.o: defs.c defs.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) defs.c | ||
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| dist.o: dist.c dist.h $(DEPS) $(DIST_DEPS) | ||
| $(CC) -c $(CFLAGS) dist.c | ||
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| dna.o: dna.c dna.h $(DEPS) $(DNA_DEPS) | ||
| $(CC) -c $(CFLAGS) dna.c | ||
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| ex.o: ex.c ex.h $(DEPS) $(EX_DEPS) | ||
| $(CC) -c $(CFLAGS) ex.c | ||
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| filter.o: filter.c filter.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) filter.c | ||
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| if.o: if.c if.h $(DEPS) $(IF_DEPS) | ||
| $(CC) -c $(CFLAGS) if.c | ||
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| kmer.o: kmer.c kmer.h $(DEPS) $(KMER_DEPS) | ||
| $(CC) -c $(CFLAGS) kmer.c | ||
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| keys.o: keys.c keys.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) keys.c | ||
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| levels.o: levels.c levels.h $(DEPS) $(LEVELS_DEPS) | ||
| $(CC) -c $(CFLAGS) levels.c | ||
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| lr.o: lr.c lr.h $(DEPS) $(LR_DEPS) | ||
| $(CC) -c $(CFLAGS) lr.c | ||
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| math.o: math.c math.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) math.c | ||
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| mem.o: mem.c mem.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) mem.c | ||
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| msg.o: msg.c msg.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) msg.c | ||
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| paint.o: paint.c paint.h $(DEPS) $(PAINT_DEPS) | ||
| $(CC) -c $(CFLAGS) paint.c | ||
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| param.o: param.c param.h $(DEPS) $(PARAM_DEPS) | ||
| $(CC) -c $(CFLAGS) param.c | ||
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| pmodels.o: pmodels.c pmodels.h $(DEPS) $(PMODELS_DEPS) | ||
| $(CC) -c $(CFLAGS) pmodels.c | ||
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| positions.o: positions.c positions.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) positions.c | ||
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| rand.o: rand.c rand.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) rand.c | ||
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| si.o: si.c si.h $(DEPS) $(SI_DEPS) | ||
| $(CC) -c $(CFLAGS) si.c | ||
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| stats.o: stats.c stats.h $(DEPS) | ||
| $(CC) -c $(CFLAGS) stats.c | ||
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| strings.o: strings.c strings.h $(DEPS) $(STRINGS_DEPS) | ||
| $(CC) -c $(CFLAGS) strings.c | ||
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| tolerant.o: tolerant.c tolerant.h $(DEPS) $(TOLERANT_DEPS) | ||
| $(CC) -c $(CFLAGS) tolerant.c | ||
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| vi.o: vi.c vi.h $(DEPS) $(VI_DEPS) | ||
| $(CC) -c $(CFLAGS) vi.c | ||
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