for hifiasm 3.0

Trio.h

@@ -0,0 +1,71 @@
+#ifndef __TRIO__
+#define __TRIO__
+#include <stdint.h>
+
+#define YAK_MAX_KMER     31
+#define YAK_COUNTER_BITS 10
+#define YAK_N_COUNTS     (1<<YAK_COUNTER_BITS)
+#define YAK_MAX_COUNT    ((1<<YAK_COUNTER_BITS)-1)
+
+#define YAK_BLK_SHIFT  9 // 64 bytes, the size of a cache line
+#define YAK_BLK_MASK   ((1<<(YAK_BLK_SHIFT)) - 1)
+
+#define YAK_LOAD_ALL       1
+#define YAK_LOAD_TRIOBIN1  2
+#define YAK_LOAD_TRIOBIN2  3
+
+#define YAK_MAGIC "YAK\2"
+
+typedef struct {
+	int n_shift, n_hashes;
+	uint8_t *b;
+} yak_bf_t;
+
+struct yak_ht_t;
+
+typedef struct {
+	struct yak_ht_t *h;
+	yak_bf_t *b;
+} yak_ch1_t;
+
+typedef struct {
+	int k, pre, n_hash, n_shift;
+	uint64_t tot;
+	yak_ch1_t *h;
+} yak_ch_t;
+
+
+typedef struct {
+	int max;
+	uint32_t *s;
+} tb_buf_t;
+
+
+typedef struct {
+	int k, n_threads, print_diff;
+	double ratio_thres;
+	///bseq_file_t *fp;
+	const yak_ch_t *ch;
+	tb_buf_t *buf;
+	UC_Read *bseq;
+	All_reads* seq; 
+} tb_shared_t;
+
+typedef struct {
+	int c[16];
+	int sc[2];
+	int nk;
+} tb_cnt_t;
+
+
+typedef struct {
+	int n_seq;
+	tb_shared_t *aux;
+	///bseq1_t *seq;
+	///All_reads* seq;
+	///tb_cnt_t *cnt;
+} tb_step_t;
+
+
+void trio_partition();
+#endif