xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-03 20:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

NOT WORKING!!! removed small_hash_table

Browse Source
This commit is contained in:
Heng Li
2020-03-24 00:57:00 -04:00
parent 59a9d62df9
commit 398e73022b
3 changed files with 11 additions and 218 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Makefile
+4 -5
View File
@@ -1,11 +1,11 @@
CXX= g++
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall #-fsanitize=address -fno-omit-frame-pointer#-Winline
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall
CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o #ksw2_extz2_sse.o
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
EXE= hifiasm
LIBS= -lz -lpthread -lm #-fsanitize=address -fno-omit-frame-pointer
LIBS= -lz -lpthread -lm
ifneq ($(asan),)
CXXFLAGS+=-fsanitize=address
@@ -51,7 +51,6 @@ POA.o: kvec.h kdq.h CommandLines.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 Trio.h kmer.h
kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.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
kmer.cpp
-187
View File
@@ -1,187 +0,0 @@
#include <stdio.h>
#include <stdlib.h>
#include "kmer.h"
void init_HPC_seq(HPC_seq* seq, char* str, long long l)
{
seq->i = 0;
seq->l = l;
seq->N_occ = 0;
seq->str = str;
}
void init_small_hash_table(small_hash_table* x)
{
x->size = 0;
x->buffer = NULL;
x->length = 0;
}
void clear_small_hash_table(small_hash_table* x)
{
x->length = 0;
}
void resize_small_hash_table(small_hash_table* x, uint64_t size)
{
if(size > x->size)
{
x->size = size;
x->buffer = (k_v*)realloc(x->buffer, x->size*sizeof(k_v));
}
}
void destory_small_hash_table(small_hash_table* x)
{
free(x->buffer);
}
void add_small_hash_table(small_hash_table* x, k_v* element)
{
if(x->length + 1 > x->size)
{
x->size = (x->length + 1) * 2;
x->buffer = (k_v*)realloc(x->buffer, x->size*sizeof(k_v));
}
x->buffer[x->length] = (*element);
x->length++;
}
//x > y, return 1; x < y, return -1, x == y, return 0
int compare_k_mer(k_v* x, k_v* y)
{
if(x->key.x[1] != y->key.x[1])
{
return x->key.x[1] > y->key.x[1] ? 1: -1;
}
else
{
if(x->key.x[0] != y->key.x[0])
{
return x->key.x[0] > y->key.x[0] ? 1: -1;
}
else
{
return 0;
}
}
}
int cmp_k_mer_kv(const void * a, const void * b)
{
int flag = compare_k_mer((k_v*)a, (k_v*)b);
if(flag == 0)
{
if ((*(k_v*)a).value != (*(k_v*)b).value)
{
return (*(k_v*)a).value > (*(k_v*)b).value ? 1: -1;
}
else
{
return 0;
}
}
else
{
return flag;
}
}
void sort_small_hash_table(small_hash_table* x)
{
qsort(x->buffer, x->length, sizeof(k_v), cmp_k_mer_kv);
}
inline long long firstEqual(k_v* arr, long long arrLen, k_v* key)
{
long long L = 0, R = arrLen - 1; //[L, R]
long long mid;
int flag;
while( L <= R)
{
mid = L + (R - L)/2;
flag = compare_k_mer(&(arr[mid]), key);
///arr[mid] >= key
if(flag >= 0)
{
R = mid - 1;
}
else
{
L = mid + 1;
}
}
if(L < arrLen && (flag = compare_k_mer(&(arr[L]), key) == 0))
{
return L;
}
return -1;
}
inline long long lastEqual(k_v* arr, long long arrLen, k_v* key)
{
long long L = 0, R = arrLen - 1; //[L, R]
long long mid;
int flag;
while( L <= R)
{
mid = L + (R - L)/2;
flag = compare_k_mer(&(arr[mid]), key);
///arr[mid] <= key
if(flag <= 0)
{
L = mid + 1;
}
else
{
R = mid - 1;
}
}
if(R >= 0 && ((flag = compare_k_mer(&(arr[R]), key)) == 0))
{
return R;
}
return -1;
}
int query_small_hash_table(small_hash_table* target, k_v* query, long long* l_end, long long* r_end)
{
(*l_end) = -1;
(*r_end) = -1;
long long left_end;
long long right_end;
left_end = firstEqual(target->buffer, target->length, query);
if(left_end != -1)
{
right_end = lastEqual(target->buffer + left_end, target->length - left_end, query) + left_end;
(*l_end) = left_end;
(*r_end) = right_end;
if(right_end == -1)
{
fprintf(stderr, "error\n");
}
return right_end - left_end + 1;
}
return 0;
}
kmer.h
+7 -26
View File
@@ -8,38 +8,12 @@
#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
/****************************may have bugs********************************/
typedef struct
{
//can represent at most 64-mer
uint64_t x[4];
} Hash_code;
typedef struct {
Hash_code key; ///k-mer itself
uint64_t value; ///offset
} k_v;
typedef struct {
k_v* buffer;
uint32_t size;
uint32_t length;
} small_hash_table;
void init_small_hash_table(small_hash_table* x);
void clear_small_hash_table(small_hash_table* x);
void resize_small_hash_table(small_hash_table* x, uint64_t size);
void destory_small_hash_table(small_hash_table* x);
void add_small_hash_table(small_hash_table* x, k_v* element);
void sort_small_hash_table(small_hash_table* x);
int compare_k_mer(k_v* x, k_v* y);
int query_small_hash_table(small_hash_table* target, k_v* query, long long* l_end, long long* r_end);
typedef struct
{
char* str;
@@ -49,6 +23,13 @@ typedef struct
} HPC_seq;
inline void init_HPC_seq(HPC_seq* seq, char* str, long long l)
{
seq->i = 0;
seq->l = l;
seq->N_occ = 0;
seq->str = str;
}
inline uint64_t get_HPC_code(HPC_seq* seq, uint64_t* end_pos)
{