NOT WORKING!!! added all k-mer counter

yak-bbf.cpp

@@ -0,0 +1,42 @@
+#include <stdlib.h>
+#include <string.h>
+#include "yak.h"
+
+yak_bf_t *yak_bf_init(int n_shift, int n_hashes)
+{
+	yak_bf_t *b;
+	void *ptr = 0;
+	if (n_shift + YAK_BLK_SHIFT > 64 || n_shift < YAK_BLK_SHIFT) return 0;
+	CALLOC(b, 1);
+	b->n_shift = n_shift;
+	b->n_hashes = n_hashes;
+	posix_memalign(&ptr, 1<<(YAK_BLK_SHIFT-3), 1ULL<<(n_shift-3));
+	b->b = (uint8_t*)ptr;
+	bzero(b->b, 1ULL<<(n_shift-3));
+	return b;
+}
+
+void yak_bf_destroy(yak_bf_t *b)
+{
+	if (b == 0) return;
+	free(b->b); free(b);
+}
+
+int yak_bf_insert(yak_bf_t *b, uint64_t hash)
+{
+	int x = b->n_shift - YAK_BLK_SHIFT;
+	uint64_t y = hash & ((1ULL<<x) - 1);
+	int h1 = hash >> x & YAK_BLK_MASK;
+	int h2 = hash >> b->n_shift & YAK_BLK_MASK;
+	uint8_t *p = &b->b[y<<(YAK_BLK_SHIFT-3)];
+	int i, z = h1, cnt = 0;
+	if ((h2&31) == 0) h2 = (h2 + 1) & YAK_BLK_MASK; // otherwise we may repeatedly use a few bits
+	for (i = 0; i < b->n_hashes; z = (z + h2) & YAK_BLK_MASK) {
+		uint8_t *q = &p[z>>3], u;
+		u = 1<<(z&7);
+		cnt += !!(*q & u);
+		*q |= u;
+		++i;
+	}
+	return cnt;
+}