minigraph-chain code-base

at-cg · Jul 14, 2022 · 20aca28 · 20aca28
1 parent 886f091
commit 20aca28
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Showing 13 changed files with 1,440 additions and 17 deletions.
diff --git a/Makefile b/Makefile
@@ -1,35 +1,34 @@
-CC=			gcc
-CFLAGS=		-g -Wall -Wc++-compat -std=c99 -msse4 -O3
-CPPFLAGS=
+CXX=			g++
+CPPFLAGS=		-g -Wall -std=c++2a -march=native -O3 -w
 INCLUDES=
 OBJS=		kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o \
             sketch.o misc.o bseq.o options.o shortk.o miniwfa.o \
 			index.o lchain.o gchain1.o galign.o gcmisc.o map-algo.o cal_cov.o \
-			format.o gmap.o ggsimple.o ggen.o asm-call.o
+			format.o gmap.o ggsimple.o ggen.o asm-call.o graphUtils.o
 PROG=		minigraph
-LIBS=		-lz -lpthread -lm
+LIBS=		-lz -lpthread -lm -fopenmp
 
 ifneq ($(asan),)
-	CFLAGS+=-fsanitize=address
+	CPPFLAGS+=-fsanitize=address
 	LIBS+=-fsanitize=address -ldl
 endif
 
 .SUFFIXES:.c .o
 .PHONY:all clean depend
 
 .c.o:
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+		$(CXX) -c $(CPPFLAGS) $(INCLUDES) $< -o $@
 
 all:$(PROG)
 
 minigraph:$(OBJS) main.o
-		$(CC) $(CFLAGS) $^ -o $@ $(LIBS)
+		$(CXX) $(CPPFLAGS) $^ -o $@ $(LIBS)
 
 clean:
 		rm -fr gmon.out *.o a.out $(PROG) *~ *.a *.dSYM
 
 depend:
-		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)
+		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CPPFLAGS) $(DFLAGS) -- *.c)
 
 # DO NOT DELETE
 
@@ -57,10 +56,11 @@ kalloc.o: kalloc.h
 kthread.o: kthread.h
 lchain.o: mgpriv.h minigraph.h gfa.h kalloc.h krmq.h
 main.o: mgpriv.h minigraph.h gfa.h gfa-priv.h sys.h ketopt.h
-map-algo.o: kalloc.h mgpriv.h minigraph.h gfa.h khashl.h ksort.h
+map-algo.o: kalloc.h mgpriv.h minigraph.h gfa.h khashl.h ksort.h graphUtils.h
 miniwfa.o: miniwfa.h kalloc.h
 misc.o: mgpriv.h minigraph.h gfa.h ksort.h
 options.o: mgpriv.h minigraph.h gfa.h sys.h
 shortk.o: mgpriv.h minigraph.h gfa.h ksort.h kavl.h algo.h khashl.h kalloc.h
 sketch.o: kvec-km.h kalloc.h mgpriv.h minigraph.h gfa.h
 sys.o: sys.h
+graphUtils.o: graphUtils.h
diff --git a/gfa-aug.c b/gfa-aug.c
@@ -195,6 +195,7 @@ void gfa_augment(gfa_t *g, int32_t n_ins, const gfa_ins_t *ins, int32_t n_ctg, c
 static int32_t gfa_ins_shrink_semi(const gfa_t *g, int32_t pen, uint32_t v, int32_t voff, int32_t coff, uint32_t vv, int32_t vend, int32_t cend, const char *seq)
 {
 	int32_t i, j, l, dir, score, max, max_l;
+	extern unsigned char gfa_comp_table[256];
 	if (cend == coff) return 0;
 	dir = cend > coff? +1 : -1;
 	for (i = coff, j = voff, l = max_l = 0, score = max = 0; i != cend; i += dir, j += dir) {

diff --git a/gfa-bbl.c b/gfa-bbl.c
@@ -204,6 +204,7 @@ typedef struct {
 static void bb_write_seq(const gfa_t *g, int32_t n, const uint32_t *v, int32_t l_seq, char *seq)
 {
 	int32_t k, l;
+	extern unsigned char gfa_comp_table[256];
 	for (k = n - 1, l = 0; k >= 0; --k) {
 		const gfa_seg_t *s = &g->seg[v[k]>>1];
 		if (v[k]&1) {

diff --git a/gfa-ed.c b/gfa-ed.c
@@ -23,6 +23,7 @@ void gfa_edopt_init(gfa_edopt_t *opt)
 
 gfa_edseq_t *gfa_edseq_init(const gfa_t *g)
 {
+	extern unsigned char gfa_comp_table[256];
 	uint32_t i, n_vtx = gfa_n_vtx(g);
 	gfa_edseq_t *es;
 	GFA_MALLOC(es, n_vtx);

diff --git a/gfa.h b/gfa.h
@@ -114,7 +114,7 @@ typedef struct {
 } gfa_ins_t;
 
 extern int gfa_verbose;
-extern unsigned char gfa_comp_table[256];
+// extern unsigned char gfa_comp_table[256];
 
 #ifdef __cplusplus
 extern "C" {