xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-08 01:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

renamed files for code cleanup

Browse Source
This commit is contained in:
Heng Li
2020-03-25 19:59:17 -04:00
parent 5a6b97145a
commit 716713685c
11 changed files with 83 additions and 80 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Assembly.cpp
+1 -1
View File
@@ -9,7 +9,7 @@
#include "POA.h"
#include "Correct.h"
#include "Output.h"
#include "yak.h"
#include "htab.h"
Total_Count_Table TCB;
Total_Pos_Table PCB;
Hash_Table.h
+1 -1
View File
@@ -2,7 +2,7 @@
#define __HASHTABLE__
#include "khashl.h"
#include "kmer.h"
#include "yak.h"
#include "htab.h"
KHASHL_MAP_INIT(static inline, Count_Table, ha_ct, uint64_t, int, kh_hash_dummy, kh_eq_generic)
KHASHL_MAP_INIT(static inline, Pos_Table, ha_pt, uint64_t, uint64_t, kh_hash_dummy, kh_eq_generic)
Makefile
+12 -13
View File
@@ -4,7 +4,7 @@ CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o \
yak-bbf.o yak-count.o hist.o sketch.o yak-sys.o
htab.o hist.o sketch.o sys.o
EXE= hifiasm
LIBS= -lz -lpthread -lm
@@ -33,30 +33,29 @@ depend:
# DO NOT DELETE
Assembly.o: Assembly.h CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h
Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h yak.h POA.h Correct.h
Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h htab.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h yak.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h htab.h
Correct.o: Levenshtein_distance.h POA.h Assembly.h
Hash_Table.o: Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
Hash_Table.o: kvec.h kdq.h CommandLines.h yak.h Correct.h
Hash_Table.o: kvec.h kdq.h CommandLines.h htab.h Correct.h
Hash_Table.o: Levenshtein_distance.h POA.h ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h yak.h Correct.h
Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h htab.h Correct.h
Overlaps.o: Levenshtein_distance.h POA.h
POA.o: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h yak.h Correct.h Levenshtein_distance.h
POA.o: kvec.h kdq.h CommandLines.h htab.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h yak.h
hist.o: yak.h
Trio.o: CommandLines.h htab.h
hist.o: htab.h
htab.o: kthread.h khashl.h kseq.h htab.h CommandLines.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h yak.h
sketch.o: kvec.h yak.h
yak-bbf.o: yak.h
yak-count.o: CommandLines.h yak.h khashl.h kthread.h kseq.h
yak-sys.o: yak.h
main.o: Assembly.h Levenshtein_distance.h htab.h
sketch.o: kvec.h htab.h
sys.o: htab.h
Trio.cpp
+1 -1
View File
@@ -6,7 +6,7 @@
#include "khashl.h" // hash table
#include "kthread.h"
#include "Process_Read.h"
#include "yak.h"
#include "htab.h"
#include "CommandLines.h"
#define YAK_MAX_KMER 31
hist.cpp
+1 -1
View File
@@ -1,5 +1,5 @@
#include <stdio.h>
#include "yak.h"
#include "htab.h"
static void yak_hist_line(int c, int x, int exceed, int64_t cnt)
{
yak-count.cpp → htab.cpp
+62 -7
View File
@@ -7,7 +7,7 @@
#include "kthread.h"
#include "khashl.h"
#include "kseq.h"
#include "yak.h"
#include "htab.h"
#include "CommandLines.h"
#define YAK_COUNTER_BITS 12
@@ -57,6 +57,54 @@ void yak_copt_init(yak_copt_t *o)
o->chunk_size = 10000000;
}
/************************
* Blocked bloom filter *
************************/
typedef struct {
int n_shift, n_hashes;
uint8_t *b;
} yak_bf_t;
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;
}
/********************
* Count hash table *
********************/
@@ -306,7 +354,7 @@ typedef struct {
ha_mz1_t *b;
} ch_buf_t;
static inline void ch_insert_buf(ch_buf_t *buf, int p, uint64_t y) // insert a k-mer $y to a linear buffer
static inline void ct_insert_buf(ch_buf_t *buf, int p, uint64_t y) // insert a k-mer $y to a linear buffer
{
int pre = y & ((1<<p) - 1);
ch_buf_t *b = &buf[pre];
@@ -340,7 +388,7 @@ static void count_seq_buf(ch_buf_t *buf, int k, int p, int len, const char *seq)
x[2] = x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift;
x[3] = x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift;
if (++l >= k)
ch_insert_buf(buf, p, yak_hash_long(x));
ct_insert_buf(buf, p, yak_hash_long(x));
} else l = 0, x[0] = x[1] = x[2] = x[3] = 0; // if there is an "N", restart
}
}
@@ -358,7 +406,7 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
x[2] = x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift;
x[3] = x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift;
if (++l >= k)
ch_insert_buf(buf, p, yak_hash_long(x));
ct_insert_buf(buf, p, yak_hash_long(x));
last = c;
}
} else l = 0, last = -1, x[0] = x[1] = x[2] = x[3] = 0; // if there is an "N", restart
@@ -375,6 +423,8 @@ typedef struct { // global data structure for kt_pipeline()
const yak_copt_t *opt;
const void *flt_tab;
int create_new, is_store;
uint64_t batch_offset;
uint64_t n_base;
kseq_t *ks;
ha_ct_t *ct;
ha_pt_t *pt;
@@ -405,7 +455,7 @@ static void worker_for_mz(void *data, long i, int tid)
st_data_t *s = (st_data_t*)data;
ha_mz1_v *b = &s->mz_buf[tid];
s->mz_buf[tid].n = 0;
ha_sketch(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, 0, s->p->opt->is_HPC, b, s->p->flt_tab);
ha_sketch(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->p->batch_offset + i, s->p->opt->is_HPC, b, s->p->flt_tab);
s->mz[i].n = s->mz[i].m = b->n;
MALLOC(s->mz[i].a, b->n);
memcpy(s->mz[i].a, b->a, b->n * sizeof(ha_mz1_t));
@@ -421,7 +471,11 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
s->p = p;
while ((ret = kseq_read(p->ks)) >= 0) {
int l = p->ks->seq.l;
if (l < p->opt->k) continue;
if (p->batch_offset + s->n_seq >= (1<<28) - 1) {
fprintf(stderr, "ERROR: this implementation supports no more than %d reads\n", (1<<28) - 1);
exit(1);
}
p->n_base += l;
if (s->n_seq == s->m_seq) {
s->m_seq = s->m_seq < 16? 16 : s->m_seq + (s->m_seq>>1);
REALLOC(s->len, s->m_seq);
@@ -473,7 +527,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
} else {
for (i = 0; i < s->n_seq; ++i)
for (j = 0; j < s->mz[i].n; ++j)
ch_insert_buf(s->buf, p->opt->pre, s->mz[i].a[j].x);
ct_insert_buf(s->buf, p->opt->pre, s->mz[i].a[j].x);
}
for (i = 0; i < s->n_seq; ++i) {
free(s->mz[i].a);
@@ -494,6 +548,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
free(s->buf[i].a);
}
p->ct->tot += n_ins;
p->batch_offset += s->n_seq;
free(s->buf);
fprintf(stderr, "[M::%s::%.3f*%.2f] processed %d sequences; %ld distinct k-mers in the hash table\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), s->n_seq, (long)p->ct->tot);
yak.h → htab.h
+2 -11
View File
@@ -1,5 +1,5 @@
#ifndef __YAK_H__
#define __YAK_H__
#ifndef __HA_HTAB_H__
#define __HA_HTAB_H__
#define __STDC_LIMIT_MACROS
#include <stdint.h>
@@ -17,11 +17,6 @@ typedef struct {
typedef struct { uint32_t n, m; ha_mz1_t *a; } ha_mz1_v;
typedef struct {
int n_shift, n_hashes;
uint8_t *b;
} yak_bf_t;
extern const unsigned char seq_nt4_table[256];
int ha_ft_isflt(const void *hh, uint64_t y);
@@ -37,10 +32,6 @@ long yak_peakrss(void);
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf);
int yak_analyze_count(int n_cnt, const int64_t *cnt, int *peak_het);
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;
main.cpp
+1 -1
View File
@@ -4,7 +4,7 @@
#include "Process_Read.h"
#include "Assembly.h"
#include "Levenshtein_distance.h"
#include "yak.h"
#include "htab.h"
int main(int argc, char *argv[])
{
sketch.cpp
+1 -1
View File
@@ -3,7 +3,7 @@
#include <assert.h>
#include <string.h>
#include "kvec.h"
#include "yak.h"
#include "htab.h"
typedef struct { // a simplified version of kdq
int front, count;
yak-sys.cpp → sys.cpp
+1 -1
View File
@@ -1,6 +1,6 @@
#include <sys/resource.h>
#include <sys/time.h>
#include "yak.h"
#include "htab.h"
int yak_verbose = 3;
yak-bbf.cpp
-42
View File
@@ -1,42 +0,0 @@
#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;
}