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optimise
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@hasindu2008
hasindu2008 committed May 19, 2024
1 parent d496200 commit cd0b4f8
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Showing 2 changed files with 89 additions and 56 deletions.
54 changes: 27 additions & 27 deletions src/slow5.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1001,7 +1001,7 @@ void *slow5_hdr_to_mem(struct slow5_hdr *header, enum slow5_fmt format, slow5_pr
len += sizeof version->patch;
memcpy(mem + len, &record_comp, sizeof record_comp);
len += sizeof record_comp;
memcpy(mem + len, &header->num_read_groups, sizeof header->num_read_groups); SLOW5_BYTE_SWAP_VOID(mem + len, sizeof header->num_read_groups);
SLOW5_MEMCPY(mem + len, &header->num_read_groups, sizeof header->num_read_groups); // SLOW5_BYTE_SWAP_VOID(mem + len, sizeof header->num_read_groups);
len += sizeof header->num_read_groups;
memcpy(mem + len, &signal_comp, sizeof signal_comp);
len += sizeof signal_comp;
Expand Down Expand Up @@ -1145,7 +1145,7 @@ void *slow5_hdr_to_mem(struct slow5_hdr *header, enum slow5_fmt format, slow5_pr
mem[len] = '\0';
} else if (format == SLOW5_FORMAT_BINARY) { //write the header size in bytes (which was skipped previously)
header_size = len - (SLOW5_BINARY_HDR_SIZE_OFFSET + sizeof header_size);
memcpy(mem + SLOW5_BINARY_HDR_SIZE_OFFSET, &header_size, sizeof header_size); SLOW5_BYTE_SWAP_VOID(mem + SLOW5_BINARY_HDR_SIZE_OFFSET, sizeof header_size);
SLOW5_MEMCPY(mem + SLOW5_BINARY_HDR_SIZE_OFFSET, &header_size, sizeof header_size); //SLOW5_BYTE_SWAP_VOID(mem + SLOW5_BINARY_HDR_SIZE_OFFSET, sizeof header_size);
}

if (n != NULL) {
Expand Down Expand Up @@ -2817,8 +2817,8 @@ int slow5_rec_parse(char *read_mem, size_t read_size, const char *read_id, struc

case COL_read_id:
size = sizeof read->read_id_len;
memcpy(&read->read_id_len, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->read_id_len);
SLOW5_MEMCPY(&read->read_id_len, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->read_id_len);
offset += size;

size = read->read_id_len * sizeof *read->read_id;
Expand All @@ -2844,43 +2844,43 @@ int slow5_rec_parse(char *read_mem, size_t read_size, const char *read_id, struc

case COL_read_group:
size = sizeof read->read_group;
memcpy(&read->read_group, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->read_group);
SLOW5_MEMCPY(&read->read_group, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->read_group);
offset += size;
break;

case COL_digitisation:
size = sizeof read->digitisation;
memcpy(&read->digitisation, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->digitisation);
SLOW5_MEMCPY(&read->digitisation, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->digitisation);
offset += size;
break;

case COL_offset:
size = sizeof read->offset;
memcpy(&read->offset, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->offset);
SLOW5_MEMCPY(&read->offset, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->offset);
offset += size;
break;

case COL_range:
size = sizeof read->range;
memcpy(&read->range, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->range);
SLOW5_MEMCPY(&read->range, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->range);
offset += size;
break;

case COL_sampling_rate:
size = sizeof read->sampling_rate;
memcpy(&read->sampling_rate, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->sampling_rate);
SLOW5_MEMCPY(&read->sampling_rate, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->sampling_rate);
offset += size;
break;

case COL_len_raw_signal:
size = sizeof read->len_raw_signal;
memcpy(&read->len_raw_signal, read_mem + offset, size);
SLOW5_BYTE_SWAP(&read->len_raw_signal);
SLOW5_MEMCPY(&read->len_raw_signal, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&read->len_raw_signal);
offset += size;
break;

Expand Down Expand Up @@ -3103,8 +3103,8 @@ static int slow5_rec_aux_parse(char *tok, char *read_mem, uint64_t offset, size_
if (SLOW5_IS_PTR(aux_meta->types[i])) {
/* Type is an array */
size = sizeof len;
memcpy(&len, read_mem + offset, size);
SLOW5_BYTE_SWAP(&len);
SLOW5_MEMCPY(&len, read_mem + offset, size);
//SLOW5_BYTE_SWAP(&len);
offset += size;
}

Expand Down Expand Up @@ -3956,19 +3956,19 @@ void *slow5_rec_to_mem(struct slow5_rec *read, struct slow5_aux_meta *aux_meta,
mem = (char *) malloc(cap * sizeof *mem);
SLOW5_MALLOC_CHK(mem);

memcpy(mem + curr_len, &read->read_id_len, sizeof read->read_id_len); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->read_id_len);
SLOW5_MEMCPY(mem + curr_len, &read->read_id_len, sizeof read->read_id_len); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->read_id_len);
curr_len += sizeof read->read_id_len;
memcpy(mem + curr_len, read->read_id, read->read_id_len * sizeof *read->read_id);
curr_len += read->read_id_len * sizeof *read->read_id;
memcpy(mem + curr_len, &read->read_group, sizeof read->read_group); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->read_group);
SLOW5_MEMCPY(mem + curr_len, &read->read_group, sizeof read->read_group); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->read_group);
curr_len += sizeof read->read_group;
memcpy(mem + curr_len, &read->digitisation, sizeof read->digitisation); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->digitisation);
SLOW5_MEMCPY(mem + curr_len, &read->digitisation, sizeof read->digitisation); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->digitisation);
curr_len += sizeof read->digitisation;
memcpy(mem + curr_len, &read->offset, sizeof read->offset); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->offset);
SLOW5_MEMCPY(mem + curr_len, &read->offset, sizeof read->offset); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->offset);
curr_len += sizeof read->offset;
memcpy(mem + curr_len, &read->range, sizeof read->range); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->range);
SLOW5_MEMCPY(mem + curr_len, &read->range, sizeof read->range); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->range);
curr_len += sizeof read->range;
memcpy(mem + curr_len, &read->sampling_rate, sizeof read->sampling_rate); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->sampling_rate);
SLOW5_MEMCPY(mem + curr_len, &read->sampling_rate, sizeof read->sampling_rate); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->sampling_rate);
curr_len += sizeof read->sampling_rate;

size_t bytes_raw_sig = read->len_raw_signal * sizeof *read->raw_signal;
Expand All @@ -3988,7 +3988,7 @@ void *slow5_rec_to_mem(struct slow5_rec *read, struct slow5_aux_meta *aux_meta,
read->raw_signal = (int16_t *) raw_sig_svb;
}

memcpy(mem + curr_len, &read->len_raw_signal, sizeof read->len_raw_signal); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->len_raw_signal);
SLOW5_MEMCPY(mem + curr_len, &read->len_raw_signal, sizeof read->len_raw_signal); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof read->len_raw_signal);
curr_len += sizeof read->len_raw_signal;
memcpy(mem + curr_len, read->raw_signal, bytes_raw_sig); SLOW5_BYTE_SWAP_ARRAY_VOID(mem + curr_len, sizeof *read->raw_signal, read->len_raw_signal);
curr_len += bytes_raw_sig;
Expand Down Expand Up @@ -4018,7 +4018,7 @@ void *slow5_rec_to_mem(struct slow5_rec *read, struct slow5_aux_meta *aux_meta,
mem = (char *) realloc(mem, cap);
SLOW5_MALLOC_CHK(mem);
}
memcpy(mem + curr_len, &aux_data.len, sizeof aux_data.len); SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof aux_data.len);
SLOW5_MEMCPY(mem + curr_len, &aux_data.len, sizeof aux_data.len); //SLOW5_BYTE_SWAP_VOID(mem + curr_len, sizeof aux_data.len);
curr_len += sizeof aux_data.len;

} else if (curr_len + aux_data.bytes >= cap) { // Realloc if necessary
Expand Down Expand Up @@ -4059,7 +4059,7 @@ void *slow5_rec_to_mem(struct slow5_rec *read, struct slow5_aux_meta *aux_meta,
uint8_t *comp_mem_full = (uint8_t *) malloc(sizeof record_size + record_size);
SLOW5_MALLOC_CHK(comp_mem_full);
// Copy size of compressed record
memcpy(comp_mem_full, &record_size, sizeof record_size); SLOW5_BYTE_SWAP_VOID(comp_mem_full, sizeof record_size);
SLOW5_MEMCPY(comp_mem_full, &record_size, sizeof record_size); //SLOW5_BYTE_SWAP_VOID(comp_mem_full, sizeof record_size);
// Copy compressed record
memcpy(comp_mem_full + sizeof record_size, comp_mem, record_size);
free(comp_mem);
Expand Down
91 changes: 62 additions & 29 deletions src/slow5_byte.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,36 +45,55 @@ extern "C" {

static inline void slow5_byte_swap(void *dest, const void *src, size_t size){
if(size==2){
char tmp0 = ((char*)src)[0];
char tmp1 = ((char*)src)[1];
((char*)dest)[0] = tmp1;
((char*)dest)[1] = tmp0;
uint16_t tmp = ((uint16_t*)src)[0];
tmp = (tmp << 8) | (tmp >> 8);
((uint16_t*)dest)[0] = tmp;

// char tmp0 = ((char*)src)[0];
// char tmp1 = ((char*)src)[1];
// ((char*)dest)[0] = tmp1;
// ((char*)dest)[1] = tmp0;

} else if(size==4){
char tmp0 = ((char*)src)[0];
char tmp1 = ((char*)src)[1];
char tmp2 = ((char*)src)[2];
char tmp3 = ((char*)src)[3];
((char*)dest)[0] = tmp3;
((char*)dest)[1] = tmp2;
((char*)dest)[2] = tmp1;
((char*)dest)[3] = tmp0;

uint32_t tmp = ((uint32_t*)src)[0];
tmp = (tmp >> 24) | ((tmp << 8) & 0x00FF0000) | ((tmp >> 8) & 0x0000FF00) | (tmp << 24);
((uint32_t*)dest)[0] = tmp;

// char tmp0 = ((char*)src)[0];
// char tmp1 = ((char*)src)[1];
// char tmp2 = ((char*)src)[2];
// char tmp3 = ((char*)src)[3];
// ((char*)dest)[0] = tmp3;
// ((char*)dest)[1] = tmp2;
// ((char*)dest)[2] = tmp1;
// ((char*)dest)[3] = tmp0;

} else if(size==8){
char tmp0 = ((char*)src)[0];
char tmp1 = ((char*)src)[1];
char tmp2 = ((char*)src)[2];
char tmp3 = ((char*)src)[3];
char tmp4 = ((char*)src)[4];
char tmp5 = ((char*)src)[5];
char tmp6 = ((char*)src)[6];
char tmp7 = ((char*)src)[7];
((char*)dest)[0] = tmp7;
((char*)dest)[1] = tmp6;
((char*)dest)[2] = tmp5;
((char*)dest)[3] = tmp4;
((char*)dest)[4] = tmp3;
((char*)dest)[5] = tmp2;
((char*)dest)[6] = tmp1;
((char*)dest)[7] = tmp0;

uint64_t tmp = ((uint64_t*)src)[0];
tmp = (tmp >> 56) | ((tmp << 40) & 0x00FF000000000000) | ((tmp << 24) & 0x0000FF0000000000) |
((tmp << 8) & 0x000000FF00000000) | ((tmp >> 8) & 0x00000000FF000000) |
((tmp >> 24) & 0x0000000000FF0000) | ((tmp >> 40) & 0x000000000000FF00) | (tmp << 56);
((uint64_t*)dest)[0] = tmp;


// char tmp0 = ((char*)src)[0];
// char tmp1 = ((char*)src)[1];
// char tmp2 = ((char*)src)[2];
// char tmp3 = ((char*)src)[3];
// char tmp4 = ((char*)src)[4];
// char tmp5 = ((char*)src)[5];
// char tmp6 = ((char*)src)[6];
// char tmp7 = ((char*)src)[7];
// ((char*)dest)[0] = tmp7;
// ((char*)dest)[1] = tmp6;
// ((char*)dest)[2] = tmp5;
// ((char*)dest)[3] = tmp4;
// ((char*)dest)[4] = tmp3;
// ((char*)dest)[5] = tmp2;
// ((char*)dest)[6] = tmp1;
// ((char*)dest)[7] = tmp0;
}
}

Expand Down Expand Up @@ -138,10 +157,23 @@ static inline int slow5_fread_bigend(void *ptr, size_t size, size_t nitems, FILE
#define SLOW5_FWRITE(ptr, size, nitems, stream) \
( (slow5_bigend) ? (slow5_fwrite_bigend((ptr), (size), (nitems), (stream))) : (fwrite((ptr), (size), (nitems), (stream))) )


#define SLOW5_FREAD(ptr, size, nitems, stream) \
( (slow5_bigend) ? (slow5_fread_bigend((ptr), (size), (nitems), (stream))) : (fread((ptr), (size), (nitems), (stream))) )

static inline void *slow5_memcpy_bigend(void *dest, const void * src, size_t size) {
if(!(size==1 || size==2 || size==4 || size==8)){
fprintf(stderr,"[%s::ERROR]\033[1;31m slow5_fwrite_bigend is only implemented for data types of size %zu\033[0m\n",__func__,size);
fprintf(stderr,"At %s:%d\n", __FILE__, __LINE__-2);
exit(EXIT_FAILURE);
}
slow5_byte_swap((dest), (src), (size));
return (dest);
}

#define SLOW5_MEMCPY(dest, src, size) \
( (slow5_bigend) ? (slow5_memcpy_bigend((dest), (src), (size))) : (memcpy((dest), (src), (size))) )


#define SLOW5_BYTE_SWAP(ptr) \
if(slow5_bigend){ \
int size = sizeof(*(ptr)); \
Expand Down Expand Up @@ -188,6 +220,7 @@ static inline int slow5_fread_bigend(void *ptr, size_t size, size_t nitems, FILE
fprintf(stderr,"At %s:%d\n", __FILE__, __LINE__); \
}\


#ifdef __cplusplus
}
#endif /* _cplusplus */
Expand Down

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