a bit code cleanup

main.cpp

@@ -18,7 +18,7 @@ int main(int argc, char *argv[])
 	yak_reset_realtime();
 	flt_tab = ha_gen_flt_tab(&asm_opt);
 	ha_gen_mzidx(&asm_opt, flt_tab);
-	ha_hf_destroy(flt_tab);
+	ha_ft_destroy(flt_tab);
 	if (0) {
 	    Correct_Reads(asm_opt.number_of_round);
 	}

sketch.cpp

@@ -76,7 +76,7 @@ void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc,
 			if (l >= k && kmer_span < 256) {
 				uint64_t y;
 				y = yak_hash64_64(kmer[z<<1|0]) + yak_hash64_64(kmer[z<<1|1]);
-				if (hf == 0 || ha_hf_isflt(hf, y) == 0)
+				if (hf == 0 || ha_ft_isflt(hf, y) == 0)
 					info.x = y, info.rid = rid, info.pos = i, info.rev = z, info.span = kmer_span;
 			}
 		} else l = 0, tq.count = tq.front = 0, kmer_span = 0;

yak-count.cpp

@@ -1,37 +1,19 @@
 #include <stdint.h>
-#include "CommandLines.h"
+#include <zlib.h>
-#include "yak.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <assert.h>
+#include "kthread.h"
 #include "khashl.h"
+#include "kseq.h"
+#include "yak.h"
+#include "CommandLines.h"
 
 #define YAK_COUNTER_BITS 12
 #define YAK_N_COUNTS     (1<<YAK_COUNTER_BITS)
 #define YAK_MAX_COUNT    ((1<<YAK_COUNTER_BITS)-1)
 
-#define yak_ch_eq(a, b) ((a)>>YAK_COUNTER_BITS == (b)>>YAK_COUNTER_BITS) // lower 8 bits for counts; higher bits for k-mer
-#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)
-KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak_ch_eq)
-
-KHASHL_SET_INIT(static klib_unused, yak_hh_t, yak_hh, uint64_t, kh_hash_dummy, kh_eq_generic)
-
-typedef struct {
-	int32_t bf_shift, bf_n_hash;
-	int32_t k, w, is_HPC;
-	int32_t pre;
-	int32_t n_thread;
-	int64_t chunk_size;
-} yak_copt_t;
-
-typedef 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;
-
 const unsigned char seq_nt4_table[256] = { // translate ACGT to 0123
 	0, 1, 2, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
@@ -51,12 +33,48 @@ const unsigned char seq_nt4_table[256] = { // translate ACGT to 0123
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
 };
 
-#include <stdio.h>
+/***************************
-#include <stdlib.h>
+ * Yak specific parameters *
-#include <assert.h>
+ ***************************/
-#include "kthread.h"
 
-/*** hash table ***/
+typedef struct {
+	int32_t bf_shift, bf_n_hash;
+	int32_t k, w, is_HPC;
+	int32_t pre;
+	int32_t n_thread;
+	int64_t chunk_size;
+} yak_copt_t;
+
+void yak_copt_init(yak_copt_t *o)
+{
+	memset(o, 0, sizeof(yak_copt_t));
+	o->bf_shift = 0;
+	o->bf_n_hash = 4;
+	o->k = 31;
+	o->w = 1;
+	o->pre = YAK_COUNTER_BITS;
+	o->n_thread = 4;
+	o->chunk_size = 10000000;
+}
+
+/********************
+ * Count hash table *
+ ********************/
+
+#define yak_ch_eq(a, b) ((a)>>YAK_COUNTER_BITS == (b)>>YAK_COUNTER_BITS) // lower 8 bits for counts; higher bits for k-mer
+#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)
+KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak_ch_eq)
+
+typedef 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;
 
 static yak_ch_t *yak_ch_init(int k, int pre, int n_hash, int n_shift)
 {
@@ -207,22 +225,27 @@ static void yak_ch_shrink(yak_ch_t *h, int min, int max, int n_thread)
 		h->tot += kh_size(h->h[i].h);
 }
 
-#include <zlib.h>
+/***********************
-#include <string.h>
+ * Position hash table *
-#include "kseq.h" // FASTA/Q parser
+ ***********************/
-KSEQ_INIT(gzFile, gzread)
 
-void yak_copt_init(yak_copt_t *o)
+KHASHL_MAP_INIT(static klib_unused, yak_pt_t, yak_pt, uint64_t, uint64_t, yak_ch_hash, yak_ch_eq)
-{
+
-	memset(o, 0, sizeof(yak_copt_t));
+typedef struct {
-	o->bf_shift = 0;
+	yak_pt_t *h;
-	o->bf_n_hash = 4;
+	uint64_t n, m;
-	o->k = 31;
+	ha_seed_t *a;
-	o->w = 1;
+} ha_pt1_t;
-	o->pre = YAK_COUNTER_BITS;
+
-	o->n_thread = 4;
+typedef struct {
-	o->chunk_size = 10000000;
+	int k, pre;
-}
+	uint64_t tot;
+	ha_pt1_t *h;
+} ha_pt_t;
+
+/**********************************
+ * Buffer for counting all k-mers *
+ **********************************/
 
 typedef struct {
 	int n, m;
@@ -282,6 +305,8 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
  * K-mer counting *
  ******************/
 
+KSEQ_INIT(gzFile, gzread)
+
 typedef struct { // global data structure for kt_pipeline()
 	const yak_copt_t *opt;
 	const void *flt_tab;
@@ -452,12 +477,18 @@ yak_ch_t *ha_count(const hifiasm_opt_t *asm_opt, int is_exact, int count_all, co
 	return h;
 }
 
-static yak_hh_t *gen_hh(const yak_ch_t *h)
+/***************************
+ * High count filter table *
+ ***************************/
+
+KHASHL_SET_INIT(static klib_unused, yak_ft_t, yak_ft, uint64_t, kh_hash_dummy, kh_eq_generic)
+
+static yak_ft_t *gen_hh(const yak_ch_t *h)
 {
 	int i;
-	yak_hh_t *hh;
+	yak_ft_t *hh;
-	hh = yak_hh_init();
+	hh = yak_ft_init();
-	yak_hh_resize(hh, h->tot * 2);
+	yak_ft_resize(hh, h->tot * 2);
 	for (i = 0; i < 1<<h->pre; ++i) {
 		yak_ht_t *ht = h->h[i].h;
 		khint_t k;
@@ -465,16 +496,33 @@ static yak_hh_t *gen_hh(const yak_ch_t *h)
 			if (kh_exist(ht, k)) {
 				uint64_t y = kh_key(ht, k) >> YAK_COUNTER_BITS << h->pre | i;
 				int absent;
-				yak_hh_put(hh, y, &absent);
+				yak_ft_put(hh, y, &absent);
 			}
 		}
 	}
 	return hh;
 }
 
+int ha_ft_isflt(const void *hh, uint64_t y)
+{
+	yak_ft_t *h = (yak_ft_t*)hh;
+	khint_t k;
+	k = yak_ft_get(h, y);
+	return k == kh_end(h)? 0 : 1;
+}
+
+void ha_ft_destroy(void *h)
+{
+	yak_ft_destroy((yak_ft_t*)h);
+}
+
+/*************************
+ * High-level interfaces *
+ *************************/
+
 void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
 {
-	yak_hh_t *flt_tab;
+	yak_ft_t *flt_tab;
 	int64_t cnt[YAK_N_COUNTS];
 	int peak_hom, peak_het, cutoff;
 	yak_ch_t *h;
@@ -492,19 +540,6 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
 	return (void*)flt_tab;
 }
 
-int ha_hf_isflt(const void *hh, uint64_t y)
-{
-	yak_hh_t *h = (yak_hh_t*)hh;
-	khint_t k;
-	k = yak_hh_get(h, y);
-	return k == kh_end(h)? 0 : 1;
-}
-
-void ha_hf_destroy(void *h)
-{
-	yak_hh_destroy((yak_hh_t*)h);
-}
-
 void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
 {
 	int64_t cnt[YAK_N_COUNTS];

yak.h

@@ -11,6 +11,10 @@ typedef struct {
 	uint64_t rid:28, pos:27, rev:1, span:8;
 } ha_mz1_t;
 
+typedef struct {
+	uint64_t rid:28, pos:27, rev:1, span:8;
+} ha_seed_t;
+
 typedef struct { uint32_t n, m; ha_mz1_t *a; } ha_mz1_v;
 
 typedef struct {
@@ -20,8 +24,8 @@ typedef struct {
 
 extern const unsigned char seq_nt4_table[256];
 
-int ha_hf_isflt(const void *hh, uint64_t y);
+int ha_ft_isflt(const void *hh, uint64_t y);
-void ha_hf_destroy(void *h);
+void ha_ft_destroy(void *h);
 
 void trio_partition(void);