r200: DFS=>BFS on subgraph extraction

resolves #15

Makefile

@@ -42,7 +42,7 @@ gfa-aug.o: gfa-priv.h gfa.h ksort.h
 gfa-base.o: gfa-priv.h gfa.h kstring.h khash.h kalloc.h ksort.h
 gfa-gt.o: gfa-priv.h gfa.h khash.h kalloc.h
 gfa-io.o: kstring.h gfa-priv.h gfa.h kseq.h
-gfa-sub.o: gfa-priv.h gfa.h kalloc.h kavl.h khash.h ksort.h
-gfa-util.o: gfa-priv.h gfa.h kvec.h ksort.h
+gfa-sub.o: gfa-priv.h gfa.h kalloc.h kavl.h khash.h ksort.h kvec.h
+gfa-util.o: gfa-priv.h gfa.h kvec.h ksort.h kdq.h
 kalloc.o: kalloc.h
 main.o: ketopt.h gfa-priv.h gfa.h kseq.h

gfa-util.c

@@ -3,27 +3,31 @@
 #include "gfa-priv.h"
 #include "kvec.h"
 #include "ksort.h"
+#include "kdq.h"
+KDQ_INIT(uint64_t)
 
 void gfa_sub(gfa_t *g, int n, char *const* seg, int step)
 {
 	int32_t i;
 	int8_t *flag;
-	kvec_t(uint64_t) stack = {0,0,0};
+	kdq_t(uint64_t) *q;
 	if (n == 0) return;
+	q = kdq_init(uint64_t);
 	GFA_CALLOC(flag, g->n_seg * 2);
 	for (i = 0; i < n; ++i) {
 		int32_t s;
 		s = gfa_name2id(g, seg[i]);
 		if (s >= 0) {
-			kv_push(uint64_t, stack, (uint64_t)(s<<1|0)<<32);
-			kv_push(uint64_t, stack, (uint64_t)(s<<1|1)<<32);
+			kdq_push(uint64_t, q, ((uint64_t)s<<1|0)<<32);
+			kdq_push(uint64_t, q, ((uint64_t)s<<1|1)<<32);
 		}
 	}
 	for (i = 0; i < g->n_seg; ++i) // mark all segments to be deleted
 		g->seg[i].del = 1;
-	while (stack.n) {
-		uint64_t x = kv_pop(stack);
-		uint32_t v = x>>32, r = (uint32_t)x;
+	while (kdq_size(q) > 0) {
+		uint64_t x = *kdq_shift(uint64_t, q);
+		uint32_t v = x>>32;
+		int r = (int32_t)x;
 		if (flag[v]) continue; // already visited
 		flag[v] = 1;
 		g->seg[v>>1].del = 0;
@@ -32,13 +36,13 @@ void gfa_sub(gfa_t *g, int n, char *const* seg, int step)
 			gfa_arc_t *av = gfa_arc_a(g, v);
 			for (i = 0; i < nv; ++i) {
 				if (flag[av[i].w] == 0)
-					kv_push(uint64_t, stack, (uint64_t)av[i].w<<32 | (r + 1));
+					kdq_push(uint64_t, q, (uint64_t)av[i].w<<32 | (r + 1));
 				if (flag[av[i].w^1] == 0)
-					kv_push(uint64_t, stack, (uint64_t)(av[i].w^1)<<32 | (r + 1));
+					kdq_push(uint64_t, q, (uint64_t)(av[i].w^1)<<32 | (r + 1));
 			}
 		}
 	}
-	free(stack.a);
+	kdq_destroy(uint64_t, q);
 	free(flag);
 	gfa_arc_rm(g);
 }

gfa.h

@@ -4,7 +4,7 @@
 #include <stdio.h>
 #include <stdint.h>
 
-#define GFA_VERSION "0.4-r199-dirty"
+#define GFA_VERSION "0.4-r200-dirty"
 
 #define GFA_O_OV_EXT   0x1
 #define GFA_O_NO_SEQ   0x2