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mapper_cpe.c
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mapper_cpe.c
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#include<slave.h>
#include<simd.h>
#include<stdint.h>
#include<dma.h>
#include<assert.h>
#include "fm_define.h"
#include "/home/export/online1/swmore/opensource/cal/cal.h"
#define DMA_FAST
//#define DMA_COUNT_BYTES
#include "dma_macros.h"
//#define CPE_PROFILE
//#define INVALID_FLAG 0xffffffffffffffff
#define READ_LEN 256
#define SIMD_WIDTH 8
#define MAXERROR 10000
#define word_t uint32_t
#define WORD_BITS 32
#define READ_INT_LEN (256/16)
#define PRINT_CORE 16
//#define NO_ALIGN
#define BALANCE
#define DMA_ASYN
#define LSEED_FILTER
//#define LONG_SEED
#define SORT_POS
#define SIMD_BM
#define SIMD_BM_ASM
#define OUT_CIGAR
/*
#define index_t uint64_t
#define sindex_t uint32_t
#define half_word_t uint16_t
#define SEED_STEP 4
#define INVALID_SFLAG 0xffffffff
#define MAX_CIGAR 256
#define CIGAR_LEN 16
typedef struct ref_info{
//in
sindex_t *hash_count;
sindex_t *hash_offset;
sindex_t *hash_positions;
sindex_t *base_2bits;
sindex_t *base_3bits;
half_word_t *pos_lseeds;
sindex_t *reads_seq_len[2];
char *reads[2];
index_t reads_name_length;
index_t reads_seq_length;
index_t seed_length;
index_t errors;
index_t ref_length;
index_t cigars_per_read;
index_t cigar_avg_len;
index_t reads_num;
//out
char *cigar_buffer[2];
sindex_t *cigar_num[2];
sindex_t *ref_pos_buffer[2];
//support
index_t *cigar_ind;
index_t *unmap_ind;
index_t cur_block;
index_t cur_read;
index_t cigar_size;
index_t cigar_len;
index_t lock_read;
}ref_info_t;
*/
typedef struct hash_count{
sindex_t hash_count;
sindex_t index;
}hash_count_t;
typedef struct hash_steps{
sindex_t step;
sindex_t index;
sindex_t pos_size;
}hash_steps_t;
typedef struct seed_heap{
sindex_t index;
sindex_t pos_size;
}seed_heap_t;
typedef struct error_s{
int error;
int location;
}error_t;
typedef struct cigar_str{
//char cigar[15*MAX_CIGAR];
char *cigar;
//sindex_t location[MAX_CIGAR];
sindex_t *location;
sindex_t cigar_len;
sindex_t cigar_num;
index_t main_flag;
index_t last_flag;
index_t f_flag;
}cigar_t;
typedef struct seed_ind_s{
sindex_t loc;
sindex_t seed_ind;
}seed_ind_t;
typedef struct read_info_s{
char *read;
sindex_t *read_2bits;
sindex_t *read_seeds;
uint8_t *res_seeds;
sindex_t read_length;
}read_info_t;
#define shrw(x, b) ((x) >> (b))
#define shlw(x, b) ((x) << (b))
#define andw(x, y) ((x) & (y))
#define xorw(x, y) ((x) ^ (y))
#define orw(x, y) ((x) | (y))
#define notw(x) (~(x))
#define subw(x, y) ((x) - (y))
#define addw(x, y) ((x) + (y))
#define eqw(x, y) (~((x) ^ (y)))
#define ZEROW 0
#define ONEW 1
#ifdef CPE_PROFILE
#define CPE
#define LWPF_KERNELS K(choose_seed_pf) K(alignment_pf) K(faaw_pf) K(bmyers_pf) K(heap_pf) K(pnum_pf) K(heap_sort_pf) \
K(align_pf) K(myers_pf) K(load_refc_pf) K(shift_pf) K(cigar_pf) \
K(load_pf) K(simd_pf) K(loopf_pf) K(loopb_pf)
#define LWPF_UNIT U(MAPPING)
#include "lwpf2/lwpf2.h"
#endif
void print_ref2char(sindex_t a, sindex_t b){
index_t i = 0;
for( i = 0; i < 32; i ++){
index_t tmp = (a >> i) & 0x1;
index_t tmp1 = (b >> i) & 0x1;
tmp = (tmp | (tmp1 << 1));
switch(tmp){
case(0):
printf("%c", 'A');
break;
case(1):
printf("%c", 'C');
break;
case(2):
printf("%c", 'G');
break;
case(3):
printf("%c", 'T');
break;
}
//con >>= 2;
}
}
void print_int2char(sindex_t con){
index_t i = 0;
for( i = 0; i < 16; i ++){
index_t tmp = con & 0x3;
switch(tmp){
case(0):
printf("%c", 'A');
break;
case(1):
printf("%c", 'C');
break;
case(2):
printf("%c", 'G');
break;
case(3):
printf("%c", 'T');
break;
}
con >>= 2;
}
}
void print_hl2char(sindex_t con){
index_t i = 0;
for( i = 0; i < 16; i ++){
index_t tmp = (con >> i) & 0x1;
index_t tmp1 = (con >> (16 + i)) << 1;
tmp = (tmp | tmp1) & 0x3;
switch(tmp){
case(0):
printf("%c", 'A');
break;
case(1):
printf("%c", 'C');
break;
case(2):
printf("%c", 'G');
break;
case(3):
printf("%c", 'T');
break;
}
//con >>= 2;
}
}
inline int sprint_length(char *cigar, sindex_t rlen){
int llen = 0;
sindex_t rlen_tmp = rlen;
while(rlen_tmp != 0){
llen += 1;
rlen_tmp /= 10;
}
int lres = llen;
while(rlen != 0){
char c = '0' + (char)rlen%10;
cigar[--llen] = c;
rlen /= 10;
}
return lres;
}
void align_reads(ref_info_t *ref_info_s, sindex_t *reads_2bits, sindex_t *ref_2bits,
sindex_t *ref_length, sindex_t read_length, index_t *ref_shift, index_t *ref_pos,
cigar_t *cigar, error_t *err_loc_info, index_t valid_size){
#ifdef NO_ALIGN
return;
#endif
int iii, ii, i;
char *cigar_s;
int cigar_len = 0;
sindex_t d0_arry_64[READ_LEN];
sindex_t hp_arry_64[READ_LEN];
int route_size_whole[READ_LEN];
char route_char_whole[READ_LEN];
for(iii = 0; iii < valid_size; iii ++){
if(err_loc_info[iii].error <= ref_info_s->errors){
cigar_len = 0;
cigar_s = cigar->cigar + cigar->cigar_len;
int start_location = err_loc_info[iii].location - read_length + 1;
int tmp_err = 0;
sindex_t hmask = 0xffff0000;
sindex_t lmask = 0x0000ffff;
//printf("start loc %u %u\n", start_location, ref_pos[iii] - 4);
for(ii = 0; ii * WORD_BITS < read_length; ii ++){
int res = WORD_BITS;
sindex_t mask = 0xffffffff;
sindex_t neq_mask = 0x1;
if((ii + 1) * WORD_BITS > read_length){
res = read_length - ii * WORD_BITS;
mask >>= (32 - res);
}
sindex_t lref = (ref_2bits[(ii*2)*SIMD_WIDTH + iii] >> start_location)| (ref_2bits[(ii + 1)*2*SIMD_WIDTH + iii] << (32 - start_location));
sindex_t href = (ref_2bits[(ii*2 + 1)*SIMD_WIDTH + iii] >> start_location)| (ref_2bits[((ii + 1)*2 + 1)*SIMD_WIDTH + iii] << (32 - start_location));
sindex_t lread = reads_2bits[READ_INT_LEN + 2*ii];
sindex_t hread = reads_2bits[READ_INT_LEN + 2*ii + 1];
sindex_t xor_res = (hread ^ href) | (lread ^ lref);
xor_res &= mask;
while(xor_res != 0){
if(xor_res & neq_mask != 0){
tmp_err ++;
}
xor_res >>= 1;
}
}
if(tmp_err == err_loc_info[iii].error){
cigar_s[cigar_len++] = (char)tmp_err;
cigar_len ++;
cigar_len += sprint_length(cigar_s + cigar_len, read_length);
cigar_s[cigar_len++] = 'M';
cigar_s[1] = (char)(cigar_len - 2);
cigar->cigar_len += cigar_len;
cigar->location[cigar->cigar_num++] = ref_pos[iii] + start_location + 1;
}
if(tmp_err != err_loc_info[iii].error){
int dist_error = (int) ref_info_s->errors;
word_t band_length = 2 * (ref_info_s->errors) + 1;
word_t band_down = 2 * (ref_info_s->errors);
word_t peq[4];
int j;
word_t res = 0;
peq[0] = 0;
peq[1] = 0;
peq[2] = 0;
peq[3] = 0;
word_t tmp = (word_t)1;
word_t ref_word = 0;
word_t ref_bits = ref_shift[iii];
word_t one = 1;
for(j = 0; j< band_length; j ++){
word_t base_enc1 = (ref_2bits[iii] >> (j & 0x1f)) & 0x1;
word_t base_enc2= (ref_2bits[SIMD_WIDTH + iii] >> (j & 0x1f)) & 0x1;
word_t base_enc = base_enc1 | (base_enc2 << 1);
peq[base_enc] |= tmp;
tmp <<= 1;
}
int last_high = band_length - read_length + ref_length[iii] - band_down - 1;
word_t x = 0, vp = 0, vn = 0, d0 = 0, hn = 0, hp = 0;
word_t w_0 = ZEROW, w_1 = ONEW;
word_t i_bd = band_down;
word_t err_mask = (word_t)1;
word_t mask = (word_t)1<<(band_length - 1);
word_t base_mask = 0x3;
for(ii = 0; ii * WORD_BITS/2 < read_length; ii ++){
res = WORD_BITS/2;
if ((ii + 1) * WORD_BITS / 2 > read_length)
res = read_length - ii * WORD_BITS/2;
for (i = 0; i < res; i ++){
word_t base_enc = (reads_2bits[ii] >> (i * 2)) & base_mask;
//x = match | vn;
x = orw(peq[base_enc], vn);
//printf("%x\n", x);
//d0 = ((vp + (x & vp)) ^ vp) | x;
d0 = andw(x, vp);
d0 = addw(d0, vp);
d0 = xorw(d0, vp);
d0 = orw(d0, x);
/* hn = vp & d0; */
hn = andw(vp, d0);
/* hp = vn | ~(vp | d0); */
hp = orw(vp, d0);
hp = notw(hp);
hp = orw(vn, hp);
//y = d0 >> 1;
x = shrw(d0, 1);
//vn = y & hp;
vn = andw(x, hp);
//vp = hn | ~(y | hp);
vp = orw(x, hp);
vp = notw(vp);
vp = orw(hn, vp);
d0_arry_64[ii * WORD_BITS/2 + i] = d0;
hp_arry_64[ii * WORD_BITS/2 + i] = hp;
peq[0] = peq[0]>>1;
peq[1] = peq[1]>>1;
peq[2] = peq[2]>>1;
peq[3] = peq[3]>>1;
++i_bd;
ref_word = i_bd >> 5;
word_t base_enc1 = (ref_2bits[(ref_word*2)*SIMD_WIDTH + iii] >> (i_bd & 0x1f)) & 0x1;
word_t base_enc2= (ref_2bits[(ref_word * 2 + 1)*SIMD_WIDTH + iii] >> (i_bd & 0x1f)) & 0x1;
base_enc = base_enc1 | (base_enc2 << 1);
peq[base_enc] |= mask;
}
}
int match_site = err_loc_info[iii].location;
int site=ref_length[iii]-last_high-1;
int search_site = match_site - site;
int pre_size = 1;
char pre_char = 'N';
sindex_t mask_1 = 1;
i = read_length - 1;
int sum_err = 0;
int err = err_loc_info[iii].error;
//#define ref_read_comp(rfi, rdi, op) (((ref_2bits[(rfi/16)*SIMD_WIDTH + iii] >> (2*(rfi%16)))&0x3) op ((reads_2bits[rdi/16] >> (2*(rdi%16)))&0x3))
#define REF_BITS(rfi) ref_2bits[(rfi)*SIMD_WIDTH + iii]
#define REF_LBIT(rfi) ((REF_BITS( (rfi>>5) * 2) >> (rfi&0x1f)) & 0x1)
#define REF_HBIT(rfi) (((REF_BITS( (rfi>>5) * 2 + 1) >> (rfi&0x1f)) & 0x1) << 1)
#define ref_read_comp(rfi, rdi, op) ((REF_HBIT(rfi) | REF_LBIT (rfi)) op ((reads_2bits[rdi/16] >> (2*(rdi%16)))&0x3))
j=1;
if(((d0_arry_64[i]>>search_site)&mask_1)&&(ref_read_comp(match_site, i, ==))){
i--;
pre_size=1;
pre_char='M';
match_site--;
}
else if(!((d0_arry_64[i]>>search_site)&mask_1)&&(ref_read_comp(match_site, i, !=))){
i--;
pre_size=1;
pre_char='S';
match_site--;
sum_err++;
}
else if((hp_arry_64[i]>>search_site)&mask_1){
i--;
search_site++;
pre_size=1;
pre_char='S';
sum_err++;
start_location++;
}
else{
search_site--;
pre_size=1;
pre_char='D';
match_site--;
sum_err++;
start_location--;
}
while(i>=0){
if(sum_err==err) break;
if(((d0_arry_64[i]>>search_site)&mask_1)&&(ref_read_comp(match_site, i, ==))){
i--;
match_site--;
if(pre_char!='M'){
route_size_whole[j]=pre_size;
route_char_whole[j++]=pre_char;
pre_size=1;
pre_char='M';
}
else pre_size++;
}
else if(!((d0_arry_64[i]>>search_site)&mask_1)&&(ref_read_comp(match_site, i, !=))){
i--;
match_site--;
sum_err++;
if(pre_char!='S'){
route_size_whole[j]=pre_size;
route_char_whole[j++]=pre_char;
pre_size=1;
pre_char='S';
}
else pre_size++;
}
else if((hp_arry_64[i]>>search_site)&mask_1){
i--;
search_site++;
sum_err++;
if(pre_char!='I'){
route_size_whole[j]=pre_size;
route_char_whole[j++]=pre_char;
pre_size=1;
pre_char='I';
}
else pre_size++;
start_location++;
}
else{
search_site--;
match_site--;
sum_err++;
if(pre_char!='D'){
route_size_whole[j]=pre_size;
route_char_whole[j++]=pre_char;
pre_size=1;
pre_char='D';
}
else pre_size++;
start_location--;
}
}
route_size_whole[j]=pre_size;
route_char_whole[j++]=pre_char;
if(i>=0){
route_size_whole[j]=i+1;
route_char_whole[j++]='M';
}
if(cigar->cigar_num > 0)
if(cigar->location[cigar->cigar_num - 1] == ref_pos[iii] + start_location + 1)
continue;
int size_sm=0;
cigar_s[cigar_len++] = (char)(err_loc_info[iii].error);
cigar_len ++;
cigar->location[cigar->cigar_num++] = ref_pos[iii] + start_location + 1;
for(j=j-1; j > 0; j--){
if(route_char_whole[j]=='M'||route_char_whole[j]=='S'){
size_sm=0;
while(j > 0 && (route_char_whole[j]=='M'||route_char_whole[j]=='S')){
size_sm=size_sm+route_size_whole[j];
j--;
}
j++;
//sprintf(cigar+strlen(cigar),"%d%c",size_sm,'m');
cigar_len += sprint_length(cigar_s + cigar_len, size_sm);
cigar_s[cigar_len++]='M';
}
else{
//sprintf(cigar+strlen(cigar),"%d%c",route_size_whole[j],route_char_whole[j]);
cigar_len += sprint_length(cigar_s + cigar_len, route_size_whole[j]);
cigar_s[cigar_len++]= route_char_whole[j];
}
}
cigar_s[1] = (char)(cigar_len - 2);
cigar->cigar_len += cigar_len;
}
#undef ref_read_comp
#undef REF_BITS
#undef REF_HBIT
#undef REF_LBIT
}
}
}
void banded_myers_simd(ref_info_t *ref_info_s, sindex_t *reads_2bits, sindex_t *ref_2bits,
sindex_t *ref_length, sindex_t read_length, index_t *ref_shift, index_t *ref_pos,
error_t *err_loc_info, index_t valid_size){
int dist_error = (int) ref_info_s->errors;
word_t band_length = 2 * (ref_info_s->errors) + 1;
word_t band_down = 2 * (ref_info_s->errors);
word_t peq[4];
int iii, ii, i;
int j;
word_t res = 0;
char base[4];
base[0] = 'A';
base[1] = 'C';
base[2] = 'G';
base[3] = 'T';
for(iii = 0; iii < valid_size; iii ++){
peq[0] = 0;
peq[1] = 0;
peq[2] = 0;
peq[3] = 0;
word_t tmp = (word_t)1;
word_t base_mask = 0x3;
word_t ref_word = 0;
word_t ref_bits = ref_shift[iii];
for(j = 0; j< band_length; j ++){
word_t base_enc1 = (ref_2bits[iii] >> (j & 0x1f)) & 0x1;
word_t base_enc2= (ref_2bits[SIMD_WIDTH + iii] >> (j & 0x1f)) & 0x1;
word_t base_enc = base_enc1 | (base_enc2 << 1);
peq[base_enc] |= tmp;
tmp <<= 1;
}
int last_high = band_length - read_length + ref_length[iii] - band_down - 1;
//printf("%d\n", last_high);
word_t x = 0, vp = 0, vn = 0, d0 = 0, hn = 0, hp = 0;
//int err = read_length;
word_t w_0 = ZEROW, w_1 = ONEW;
int err = 0;
word_t i_bd = band_down;
word_t err_mask = (word_t)1;
word_t pass_flag = 1;
word_t mask = (word_t)1<<(band_length - 1);
for(ii = 0; ii * WORD_BITS/2 < read_length; ii ++){
res = WORD_BITS/2;
if ((ii + 1) * WORD_BITS / 2 > read_length)
res = read_length - ii * WORD_BITS/2;
for (i = 0; i < res; i ++){
word_t base_enc = (reads_2bits[ii] >> (i * 2)) & base_mask;
//x = match | vn;
x = orw(peq[base_enc], vn);
//if(_MYID == PRINT_CORE){
// //if(ii == 0 && i == 0)
// //printf("%x ", peq[base_enc]);
// //printf("%x ", x);
//
//}
//printf("%x\n", x);
//d0 = ((vp + (x & vp)) ^ vp) | x;
d0 = andw(x, vp);
d0 = addw(d0, vp);
d0 = xorw(d0, vp);
d0 = orw(d0, x);
/* hn = vp & d0; */
hn = andw(vp, d0);
/* hp = vn | ~(vp | d0); */
hp = orw(vp, d0);
hp = notw(hp);
hp = orw(vn, hp);
//y = d0 >> 1;
x = shrw(d0, 1);
//vn = y & hp;
vn = andw(x, hp);
//vp = hn | ~(y | hp);
vp = orw(x, hp);
vp = notw(vp);
vp = orw(hn, vp);
if(!(d0&err_mask)){
++err;
}
peq[0] = peq[0]>>1;
peq[1] = peq[1]>>1;
peq[2] = peq[2]>>1;
peq[3] = peq[3]>>1;
++i_bd;
ref_word = i_bd >> 5;
//base_enc = (ref_2bits[ref_word*SIMD_WIDTH + iii] >> ( (i_bd % 16) * 2)) & base_mask;
word_t base_enc1 = (ref_2bits[(ref_word*2)*SIMD_WIDTH + iii] >> (i_bd & 0x1f)) & 0x1;
word_t base_enc2= (ref_2bits[(ref_word * 2 + 1)*SIMD_WIDTH + iii] >> (i_bd & 0x1f)) & 0x1;
base_enc = base_enc1 | (base_enc2 << 1);
peq[base_enc] |= mask;
}
}
int site=ref_length[iii]-last_high-1;
int location = -1;
int error = MAXERROR;
if((err <= dist_error)&&(err < error)){
error = err;
location = site;
}
for(i = 0; i < last_high; i++){
err=err+((vp>>i)&(word_t)1);
err=err-((vn>>i)&(word_t)1);
if((err<=dist_error)&&(err<error)){
error = err;
location = site+i+1;
}
}
if(error > dist_error){
pass_flag = 0;
}
err_loc_info[iii].error = error;
err_loc_info[iii].location = location;
}
}
void print_simd_n(uintv8 in, sindex_t i){
uint32_t v[8];
simd_store(in, v);
printf("%x\n", v[i]);
}
//#define FIND 2907861898
void banded_myers_simd_asmv2(ref_info_t *ref_info_s, sindex_t *reads_2bits, sindex_t *ref_2bits,
sindex_t *ref_length, sindex_t read_length, index_t *ref_shift, index_t *ref_pos,
error_t *err_loc_info, index_t valid_size){
int dist_error = (int)ref_info_s->errors;
sindex_t band_length = 2 * (ref_info_s->errors) + 1;
sindex_t band_down = 2 * (ref_info_s->errors);
//uintv8 peqv[4];
// uintv8 ref_2bitsv[READ_LEN/16];
uintv8 onev = 1;
int iii, ii, i;
uintv8 base_maskv = 0x3;
uintv8 peqv_0 = 0;
uintv8 peqv_1 = 0;
sindex_t peq_mask = (1U << band_length) - 1;
uintv8 peqv_mask = peq_mask;
//sindex_t band_down_mask = (1U << band_down) - 1;
if(band_length < 32){
uintv8 tmp1;
uintv8 tmp2;
simd_load(tmp1, ref_2bits);
simd_load(tmp2, ref_2bits + SIMD_WIDTH);
peqv_0 = tmp1 & peqv_mask;
peqv_1 = tmp2 & peqv_mask;
}
uintv8 ref_2bitsv[READ_LEN / 16];
for(i = 0; i < (read_length + band_down + 31)/32; i ++){
uintv8 tmp1;
uintv8 tmp2;
uintv8 tmp3;
uintv8 tmp4;
sindex_t r_shift = band_length;
sindex_t l_shift = 32 - band_length;
simd_load(tmp1, ref_2bits + (i * 2 )*SIMD_WIDTH);
simd_load(tmp2, ref_2bits + ((i + 1)* 2)*SIMD_WIDTH);
//simd_print_int256(tmp1);
//simd_print_int256(tmp2);
asm ("vsrlw %2, %1, %0\n":"=r"(tmp1):"r"(r_shift), "r"(tmp1));
asm ("vsllw %2, %1, %0\n":"=r"(tmp2):"r"(l_shift), "r"(tmp2));
tmp3 = simd_vbisw(tmp1,tmp2);
//simd_print_int256(tmp3);
simd_load(tmp1, ref_2bits + (i * 2 + 1)*SIMD_WIDTH);
simd_load(tmp2, ref_2bits + ((i + 1) * 2 + 1)*SIMD_WIDTH);
//simd_print_int256(tmp1);
//simd_print_int256(tmp2);
asm ("vsrlw %2, %1, %0\n":"=r"(tmp1):"r"(r_shift), "r"(tmp1));
asm ("vsllw %2, %1, %0\n":"=r"(tmp2):"r"(l_shift), "r"(tmp2));
tmp4 = simd_vbisw(tmp1,tmp2);
//simd_print_int256(tmp4);
uintv8 hmaskv = 0xffff0000;
uintv8 lmaskv = 0x0000ffff;
tmp1 = simd_vandw(tmp3, lmaskv);
tmp2 = simd_vandw(tmp4, lmaskv);
//simd_print_int256(tmp1);
//simd_print_int256(tmp2);
asm ("vsllw %1, 16, %0\n":"=r"(tmp2):"r"(tmp2));
tmp1 = simd_vbisw(tmp1, tmp2);
ref_2bitsv[i*2] = tmp1;
//simd_print_int256(tmp1);
tmp1 = simd_vandw(tmp3, hmaskv);
tmp2 = simd_vandw(tmp4, hmaskv);
//simd_print_int256(tmp1);
//simd_print_int256(tmp2);
asm ("vsrlw %1, 16, %0\n":"=r"(tmp1):"r"(tmp1));
tmp1 = simd_vbisw(tmp1, tmp2);
ref_2bitsv[i*2 + 1] = tmp1;
//simd_print_int256(tmp1);
}
#ifdef CPE_PROFILE
lwpf_start(loopf_pf);
#endif
sindex_t base_mask = 0x3;
sindex_t ref_word = 0;
uintv8 xv = 0, vpv = 0, vnv = 0, d0v = 0, hnv = 0, hpv = 0;
intv8 errv = 0;
uintv8 err_maskv = (word_t)1;
sindex_t i_bd = band_down;
#ifdef CPE_PROFILE
lwpf_stop(loopf_pf);
#endif
//index_t pre_ref = 0;
//uintv8 base_refv;
//simd_load(base_refv, ref_2bits + (i_bd/16)*SIMD_WIDTH);
#ifdef CPE_PROFILE
lwpf_start(simd_pf);
#endif
sindex_t shift_band = band_length - 1;
struct {
uintv8 peqv_l, peqv_h, vp, vn, errv, peqv_mask, refv;
int i_bd, i2, read, ref_bptr, shift_band, res, pad0, pad1;
} loop_vars;
loop_vars.peqv_l = peqv_0;
loop_vars.peqv_h = peqv_1;
loop_vars.vp = vpv;
loop_vars.vn = vnv;
loop_vars.errv = errv;
loop_vars.peqv_mask = peqv_mask;
loop_vars.shift_band = shift_band;
loop_vars.i_bd = i_bd;
loop_vars.ref_bptr = ref_2bits;
asm ("wcsr %0, 0x80\n\t" : : "r"(0xAC));
asm ("wcsr %0, 0x81\n\t" : : "r"(0x80));
asm ("wcsr %0, 0x82\n\t" : : "r"(0xBE));
asm ("wcsr %0, 0x83\n\t" : : "r"(0xF1));
//sindex_t rshift = 32 - band_length;
//uintv8 refh = 0;
//uintv8 refl = 0;
for(ii = 0; ii * WORD_BITS/2 < read_length; ii ++){
sindex_t res = WORD_BITS/2;
if ((ii + 1) * WORD_BITS / 2 > read_length)
res = read_length - ii * WORD_BITS/2;
loop_vars.i2 = 0;
loop_vars.refv = ref_2bitsv[ii];
loop_vars.read = reads_2bits[ii];
//for(iii = 0; iii < res ; iii ++){
loop_vars.res = res;
uintv8 t0, t1, t2, t3, t4, t5, t6, t7, ptrs;
asm(//load pointers to PTRS
"vldd %[ptrs], 224(%[bptr])\n\t"
//peqv in t2/3
"vldd %[t3], 0(%[bptr])\n\t"
"vldd %[t4], 32(%[bptr])\n\t"
"vldd %[t6], 64(%[bptr])\n\t"
"vldd %[t7], 96(%[bptr])\n\t"
//ref in at
"vldd $at, 192(%[bptr])\n\t"
//sp for peqv_mask, bptr for errv
"vinsw $30, %[ptrs], 6, %[ptrs]\n\t"
"vinsw %[bptr], %[ptrs], 7, %[ptrs]\n\t"
"vldd $30, 160(%[bptr])\n\t"
"vldd %[bptr], 128(%[bptr])\n\t"
"1001:"
//read2bits to t0, 2i to t1
"vextw %[ptrs], 2, %[t0]\n\t"
"#vextw %[ptrs], 1, %[t1]\n\t"
//benc to t0, extend to vec"
"#ldi %[t1], 2(%[t1])\n\t"
"vshfw %[t0], %[t0], $31, %[t0]\n\t"
//peqv in t3/4
/* "vbis %[t3], %[t3], %[t4]\n\t" */
/* "vbis %[t2], %[t2], %[t3]\n\t" */
//read_1bitsv in t1/2
"vand %[t0], 1, %[t1]\n\t"
"vsrlw %[t0], 1, %[t2]\n\t"
//shift the read
"srl %[t0], 2, %[t0]\n\t"
"vinsw %[t0], %[ptrs], 2, %[ptrs]\n\t"
"vsubw $31, %[t1], %[t1]\n\t"
"vand %[t2], 1, %[t2]\n\t"
"vsubw $31, %[t2], %[t2]\n\t"
//t1, t2 for beqvl/h
"veqv %[t1], %[t3], %[t1]\n\t"
"veqv %[t2], %[t4], %[t2]\n\t"
//peqv_mask in sp
"vlog3r1 %[t1], %[t2], $30, %[t0]\n\t"
//t0->eqv t7->vn, t1->x0
"vbis %[t0], %[t7], %[t1]\n\t"
//t0->d0, t6->vp, t1->x0
"vand %[t6], %[t1], %[t0]\n\t"
"vaddw %[t0], %[t6], %[t0]\n\t"
"vlog3r2 %[t0], %[t6], %[t1], %[t0]\n\t"
//t1->hp, t2->hn, t6->vp, t7->vn, t0->d0
"vand %[t6], %[t0], %[t2]\n\t"
"vlog3r3 %[t7], %[t6], %[t0], %[t1]\n\t"
//update vp, vn, t5->x0
"vsrlw %[t0], 1, %[t5]\n\t"
"vand %[t5], %[t1], %[t7]\n\t"
"vlog3r3 %[t2], %[t5], %[t1], %[t6]\n\t"
"vlog2x2 %[t0], 1, %[t0]\n\t"
"vaddw %[bptr], %[t0], %[bptr]\n\t"
//ires->t0, bencv->t1
"#vextw %[ptrs], 0, %[t1]\n\t"
//increase i_bd by 1
"#ldi %[t1], 1(%[t1])\n\t"
"#vinsw %[t1], %[ptrs], 0, %[ptrs]\n\t"
"#srl %[t1], 4, %[t1]\n\t"
"#sll %[t1], 8, %[t1]\n\t"
"#vextw %[ptrs], 3, %[t0]\n\t"
"#addl %[t0], %[t1], %[t1]\n\t"
"#vldd %[t1], 0(%[t1])\n\t"
"#and %[ptrs], 0xf, %[t0]\n\t"
//shift peqvl/h
"vsrlw %[t3], 1, %[t3]\n\t"
"vsrlw %[t4], 1, %[t4]\n\t"
//shift bencvl/h t1/t0
"#vsrlw %[t1], %[t0], %[t1]\n\t"
"vsrlw $at, 16, %[t0]\n\t"
"#halt\n\t"
//extract shift_band to t0\n\t"
"vand $at, 1, %[t1]\n\t"
"vand %[t0], 1, %[t0]\n\t"
"vsrlw $at, 1, $at\n\t"
//"vextw %[ptrs], 4, %[t3]\n\t"
//"vsllw %[t1], %[t3], %[t1]\n\t"
//"vsllw %[t0], %[t3], %[t0]\n\t"
//extract shift_band to t2\n\t
"vextw %[ptrs], 4, %[t2]\n\t"
"vsllw %[t1], %[t2], %[t1]\n\t"
"vsllw %[t0], %[t2], %[t0]\n\t"
"vbis %[t3], %[t1], %[t3]\n\t"
"vbis %[t4], %[t0], %[t4]\n\t"
//extract res, consider jump back
"vextw %[ptrs], 5, %[t0]\n\t"
"ldi %[t0], -1(%[t0])\n\t"
"vinsw %[t0], %[ptrs], 5, %[ptrs]\n\t"
"bgt %[t0], 1001b\n\t"
//store/restore values
"vextw %[ptrs], 7, %[t0]\n\t"
"vstd %[t3], 0(%[t0])\n\t"
"vstd %[t4], 32(%[t0])\n\t"
"vstd %[t6], 64(%[t0])\n\t"
"vstd %[t7], 96(%[t0])\n\t"
"vstd %[bptr], 128(%[t0])\n\t"
"vextw %[ptrs], 6, $30\n\t"
"vinsw $30, $31, 0, $30\n\t"
"vinsw %[bptr], $31, 0, %[bptr]\n\t"
: [t0]"=&r"(t0), [t1]"=&r"(t1), [t2]"=&r"(t2), [t3]"=&r"(t3),
[t4]"=&r"(t4), [t5]"=&r"(t5), [t6]"=&r"(t6), [t7]"=&r"(t7),
[ptrs]"=&r"(ptrs)
: [bptr]"r"(&loop_vars)
: "memory"
);
}
#ifdef CPE_PROFILE
lwpf_stop(simd_pf);
lwpf_start(loopb_pf);
#endif
int err_arr[SIMD_WIDTH];
sindex_t vp_arr[SIMD_WIDTH];
sindex_t vn_arr[SIMD_WIDTH];
simd_store(loop_vars.errv, err_arr);
simd_store(loop_vars.vp, vp_arr);
simd_store(loop_vars.vn, vn_arr);
for(iii = 0; iii < valid_size; iii ++){
int last_high = band_length - read_length + ref_length[iii] - band_down - 1;
int site=ref_length[iii]-last_high-1;
int err = err_arr[iii];
sindex_t vp = vp_arr[iii];
sindex_t vn = vn_arr[iii];
//if(ref_pos[iii] == FIND - 4){
// printf("error %u\n", err);
//}
int location = -1;
int error = MAXERROR;
if((err <= dist_error)&&(err < error)){
error = err;
location = site;
}
for(i = 0; i < last_high; i++){
err=err+((vp>>i)&(word_t)1);
err=err-((vn>>i)&(word_t)1);
if((err<=dist_error)&&(err<error)){
error = err;
location = site+i+1;
}
}
err_loc_info[iii].error = error;
err_loc_info[iii].location = location;
}
#ifdef CPE_PROFILE
lwpf_stop(loopb_pf);
#endif
}
void banded_myers_simd_v(ref_info_t *ref_info_s, sindex_t *reads_2bits, sindex_t *ref_2bits,
sindex_t *ref_length, sindex_t read_length, index_t *ref_shift, index_t *ref_pos,
error_t *err_loc_info, index_t valid_size){
int dist_error = (int)ref_info_s->errors;
sindex_t band_length = 2 * (ref_info_s->errors) + 1;
sindex_t band_down = 2 * (ref_info_s->errors);
//uintv8 peqv[4];
// uintv8 ref_2bitsv[READ_LEN/16];
uintv8 onev = 1;
int iii, ii, i;
int j;
uintv8 ref_2bitsvh[READ_LEN/32];
uintv8 ref_2bitsvl[READ_LEN/32];
for(i = 0; i < (read_length + band_down + 31)/32; i ++){
uintv8 base_encvl;
uintv8 base_encvh;
simd_load(base_encvl, ref_2bits + (i * 2 )*SIMD_WIDTH);