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seed三个步骤，全部用fmt实现，而且结果一致

This commit is contained in:
zzh 2024-02-16 20:59:59 +08:00
parent 9d45fd02fb
commit 7dceae8c5d
4 changed files with 96 additions and 26 deletions
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60
bwamem.c
View File

@ -144,6 +144,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
int start_width = 1; int start_width = 1;
int split_len = (int)(opt->min_seed_len * opt->split_factor + .499); int split_len = (int)(opt->min_seed_len * opt->split_factor + .499);
int max_seed_len = 0; int max_seed_len = 0;
int start_N_num = 0, start_flag = 1;
a->mem.n = 0; a->mem.n = 0;
// char *BASE = "ACGT"; // char *BASE = "ACGT";
// for (i = 0; i < len; ++i) // for (i = 0; i < len; ++i)
@ -157,8 +158,11 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
//fprintf(fp1, "seq: %ld\n", dn++); //fprintf(fp1, "seq: %ld\n", dn++);
//fprintf(stderr, "seq: %ld\n", dn++); //fprintf(stderr, "seq: %ld\n", dn++);
//dn ++; //dn ++;
//goto third_seed;
while (x < len) { while (x < len) {
if (seq[x] < 4) { if (seq[x] < 4) {
start_flag = 0;
#ifdef SHOW_PERF #ifdef SHOW_PERF
int64_t tmp_time = realtime_msec(); int64_t tmp_time = realtime_msec();
#endif #endif
@ -172,22 +176,27 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
bwtintv_t *p = &a->mem1.a[i]; bwtintv_t *p = &a->mem1.a[i];
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info); //fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info); //fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
int slen = (uint32_t)p->info - (p->info >> 32); // seed length //int slen = (uint32_t)p->info - (p->info >> 32); // seed length
if (slen < 16) ++n16; //if (slen < 16) ++n16;
if (slen < 17) ++n17; //if (slen < 17) ++n17;
if (slen < 18) ++n18; //if (slen < 18) ++n18;
if (slen < 19) ++n19; //if (slen < 19) ++n19;
++nall; //++nall;
max_seed_len = fmax(max_seed_len, slen); max_seed_len = fmax(max_seed_len, slen);
if (slen >= opt->min_seed_len) if (slen >= opt->min_seed_len)
kv_push(bwtintv_t, a->mem, *p); kv_push(bwtintv_t, a->mem, *p);
} }
} else ++x; } else {
++x;
if (start_flag)
++start_N_num;
}
} }
// second pass: find MEMs inside a long SMEM // second pass: find MEMs inside a long SMEM
//if (max_seed_len == len) //if (max_seed_len == len - start_N_num)
//goto collect_intv_end; // goto collect_intv_end;
// goto third_seed;
old_n = a->mem.n; old_n = a->mem.n;
for (k = 0; k < old_n; ++k) { for (k = 0; k < old_n; ++k) {
bwtintv_t *p = &a->mem.a[k]; bwtintv_t *p = &a->mem.a[k];
@ -206,19 +215,20 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
bwtintv_t *p = &a->mem1.a[i]; bwtintv_t *p = &a->mem1.a[i];
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info); //fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info); //fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
int slen = (uint32_t)p->info - (p->info >> 32); //int slen = (uint32_t)p->info - (p->info >> 32);
if (slen < 16) ++n16; //if (slen < 16) ++n16;
if (slen < 17) ++n17; //if (slen < 17) ++n17;
if (slen < 18) ++n18; //if (slen < 18) ++n18;
if (slen < 19) ++n19; //if (slen < 19) ++n19;
++nall; //++nall;
if ((uint32_t)a->mem1.a[i].info - (a->mem1.a[i].info >> 32) >= opt->min_seed_len) if ((uint32_t)a->mem1.a[i].info - (a->mem1.a[i].info >> 32) >= opt->min_seed_len)
kv_push(bwtintv_t, a->mem, a->mem1.a[i]); kv_push(bwtintv_t, a->mem, a->mem1.a[i]);
} }
} }
//if (max_seed_len == len - start_N_num)
goto collect_intv_end; // goto collect_intv_end;
//goto collect_intv_end;
third_seed:
// third pass: LAST-like // third pass: LAST-like
if (opt->max_mem_intv > 0) { if (opt->max_mem_intv > 0) {
x = 0; x = 0;
@ -229,12 +239,20 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
#ifdef SHOW_PERF #ifdef SHOW_PERF
int64_t tmp_time = realtime_msec(); int64_t tmp_time = realtime_msec();
#endif #endif
x = bwt_seed_strategy1(bwt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m); //x = bwt_seed_strategy1(bwt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
x = fmt_seed_strategy1(fmt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
#ifdef SHOW_PERF #ifdef SHOW_PERF
tmp_time = realtime_msec() - tmp_time; tmp_time = realtime_msec() - tmp_time;
__sync_fetch_and_add(&time_bwt_smem1a, tmp_time); __sync_fetch_and_add(&time_bwt_smem1a, tmp_time);
#endif #endif
if (m.x[2] > 0) kv_push(bwtintv_t, a->mem, m); //bwtintv_t *p = &m;
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
if (m.x[2] > 0) {
kv_push(bwtintv_t, a->mem, m);
//bwtintv_t *p = &m;
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
}
} else { // for now, we never come to this block which is slower } else { // for now, we never come to this block which is slower
x = bwt_smem1a(bwt, len, seq, x, start_width, opt->max_mem_intv, &a->mem1, a->tmpv); x = bwt_smem1a(bwt, len, seq, x, start_width, opt->max_mem_intv, &a->mem1, a->tmpv);
for (i = 0; i < a->mem1.n; ++i) for (i = 0; i < a->mem1.n; ++i)

51
fmt_idx.c
View File

@ -854,4 +854,55 @@ fmt_smem_end:
if (tmpvec == 0 || tmpvec[0] == 0) if (tmpvec == 0 || tmpvec[0] == 0)
free(a[0].a); free(a[0].a);
return ret; return ret;
}
int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem)
{
int i, kmer_len;
bwtintv_t ik, ok1, ok2;
uint64_t qbit;
memset(mem, 0, sizeof(bwtintv_t));
if (q[x] > 3)
return x + 1;
qbit = (uint32_t)build_forward_kmer(&q[x], len - x, HASH_KMER_LEN, &kmer_len);
fmt_kmer_get(fmt, &ik, qbit, kmer_len-1); // 初始碱基位置
ik.info = x + kmer_len;
#define COND_SET_RETURN(iv, ov, start_pos, end_pos, max_intv, min_len) \
if (iv.x[2] < max_intv && end_pos - start_pos >= min_len) \
{ \
(ov) = (iv); \
(ov).info = (uint64_t)start_pos << 32 | (end_pos + 1); \
return end_pos + 1; \
}
for (i = (int)ik.info; i + 1 < len; i += 2)
{ // forward search
if (q[i] < 4 && q[i + 1] < 4)
{
fmt_extend2(fmt, &ik, &ok1, &ok2, 0, 3 - q[i], 3 - q[i + 1]);
COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
COND_SET_RETURN(ok2, *mem, x, i + 1, max_intv, min_len);
ik = ok2;
}
else if (q[i] < 4) // q[i+1] >= 4
{
fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
return i + 2;
}
else // q[i] >= 4
{
return i + 1;
}
}
if (i == len - 1) {
fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
}
return len;
} }

1
fmt_idx.h
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@ -131,4 +131,5 @@ void fmt_kmer_get(const FMTIndex *fmt, bwtintv_t *ok, uint32_t qbit, int pos);
// 找smem（seed） // 找smem（seed）
int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]); int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem);
#endif #endif

10
run.sh
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@ -4,16 +4,16 @@ thread=1
#n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq #n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
#n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq #n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
#reference=~/data/reference/human_g1k_v37_decoy.fasta #reference=~/data/reference/human_g1k_v37_decoy.fasta
n_r1=~/fastq/sn_r1.fq #n_r1=~/fastq/sn_r1.fq
n_r2=~/fastq/sn_r2.fq #n_r2=~/fastq/sn_r2.fq
#n_r1=~/fastq/tiny_n_r1.fq n_r1=~/fastq/tiny_n_r1.fq
#n_r2=~/fastq/tiny_n_r3.fq n_r2=~/fastq/tiny_n_r2.fq
#n_r1=~/fastq/diff_r1.fq #n_r1=~/fastq/diff_r1.fq
#n_r2=~/fastq/diff_r2.fq #n_r2=~/fastq/diff_r2.fq
#n_r1=~/fastq/d_r1.fq #n_r1=~/fastq/d_r1.fq
#n_r2=~/fastq/d_r2.fq #n_r2=~/fastq/d_r2.fq
reference=~/reference/human_g1k_v37_decoy.fasta reference=~/reference/human_g1k_v37_decoy.fasta
out=./fmt_all.sam out=./out.sam
#out=/dev/null #out=/dev/null
#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \ #time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \ # /home/zzh/data/reference/human_g1k_v37_decoy.fasta \