NOT WORKING!!! added all k-mer counter

yak.h

@@ -0,0 +1,68 @@
+#ifndef __YAK_H__
+#define __YAK_H__
+#include <stdint.h>
+
+#define YAK_BLK_SHIFT  9 // 64 bytes, the size of a cache line
+#define YAK_BLK_MASK   ((1<<(YAK_BLK_SHIFT)) - 1)
+
+typedef struct {
+	int n_shift, n_hashes;
+	uint8_t *b;
+} yak_bf_t;
+
+extern const unsigned char seq_nt4_table[256];
+
+void trio_partition(void);
+
+double yak_cputime(void);
+void yak_reset_realtime(void);
+double yak_realtime(void);
+long yak_peakrss(void);
+
+yak_bf_t *yak_bf_init(int n_shift, int n_hashes);
+void yak_bf_destroy(yak_bf_t *b);
+int yak_bf_insert(yak_bf_t *b, uint64_t hash);
+
+static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function
+{
+	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
+	key = key ^ key >> 24;
+	key = ((key + (key << 3)) + (key << 8)) & mask; // key * 265
+	key = key ^ key >> 14;
+	key = ((key + (key << 2)) + (key << 4)) & mask; // key * 21
+	key = key ^ key >> 28;
+	key = (key + (key << 31)) & mask;
+	return key;
+}
+
+static inline uint64_t yak_hash64_64(uint64_t key)
+{
+	key = ~key + (key << 21);
+	key = key ^ key >> 24;
+	key = (key + (key << 3)) + (key << 8);
+	key = key ^ key >> 14;
+	key = (key + (key << 2)) + (key << 4);
+	key = key ^ key >> 28;
+	key = key + (key << 31);
+	return key;
+}
+
+static inline uint64_t yak_hash_long(uint64_t x[4])
+{
+	int j = x[1] < x[3]? 0 : 1;
+	return yak_hash64_64(x[j<<1|0]) + yak_hash64_64(x[j<<1|1]);
+}
+
+#define CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr))))
+#define MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
+#define REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
+
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
+#endif // __YAK_H__