seed三个步骤，全部用fmt实现，而且结果一致
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zzh
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9d45fd02fb
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7dceae8c5d
56
bwamem.c
56
bwamem.c
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@ -144,6 +144,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
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int start_width = 1;
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int split_len = (int)(opt->min_seed_len * opt->split_factor + .499);
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int max_seed_len = 0;
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int start_N_num = 0, start_flag = 1;
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a->mem.n = 0;
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// char *BASE = "ACGT";
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// for (i = 0; i < len; ++i)
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@ -157,8 +158,11 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
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//fprintf(fp1, "seq: %ld\n", dn++);
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//fprintf(stderr, "seq: %ld\n", dn++);
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//dn ++;
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//goto third_seed;
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while (x < len) {
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if (seq[x] < 4) {
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start_flag = 0;
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#ifdef SHOW_PERF
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int64_t tmp_time = realtime_msec();
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#endif
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@ -172,21 +176,26 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
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bwtintv_t *p = &a->mem1.a[i];
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//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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int slen = (uint32_t)p->info - (p->info >> 32); // seed length
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if (slen < 16) ++n16;
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if (slen < 17) ++n17;
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if (slen < 18) ++n18;
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if (slen < 19) ++n19;
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++nall;
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//int slen = (uint32_t)p->info - (p->info >> 32); // seed length
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//if (slen < 16) ++n16;
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//if (slen < 17) ++n17;
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//if (slen < 18) ++n18;
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//if (slen < 19) ++n19;
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//++nall;
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max_seed_len = fmax(max_seed_len, slen);
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if (slen >= opt->min_seed_len)
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kv_push(bwtintv_t, a->mem, *p);
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}
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} else ++x;
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} else {
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++x;
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if (start_flag)
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++start_N_num;
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}
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}
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// second pass: find MEMs inside a long SMEM
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//if (max_seed_len == len)
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//if (max_seed_len == len - start_N_num)
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// goto collect_intv_end;
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// goto third_seed;
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old_n = a->mem.n;
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for (k = 0; k < old_n; ++k) {
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@ -206,19 +215,20 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
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bwtintv_t *p = &a->mem1.a[i];
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//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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int slen = (uint32_t)p->info - (p->info >> 32);
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if (slen < 16) ++n16;
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if (slen < 17) ++n17;
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if (slen < 18) ++n18;
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if (slen < 19) ++n19;
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++nall;
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//int slen = (uint32_t)p->info - (p->info >> 32);
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//if (slen < 16) ++n16;
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//if (slen < 17) ++n17;
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//if (slen < 18) ++n18;
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//if (slen < 19) ++n19;
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//++nall;
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if ((uint32_t)a->mem1.a[i].info - (a->mem1.a[i].info >> 32) >= opt->min_seed_len)
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kv_push(bwtintv_t, a->mem, a->mem1.a[i]);
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}
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}
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goto collect_intv_end;
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//if (max_seed_len == len - start_N_num)
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// goto collect_intv_end;
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//goto collect_intv_end;
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third_seed:
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// third pass: LAST-like
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if (opt->max_mem_intv > 0) {
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x = 0;
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@ -229,12 +239,20 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
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#ifdef SHOW_PERF
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int64_t tmp_time = realtime_msec();
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#endif
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x = bwt_seed_strategy1(bwt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
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//x = bwt_seed_strategy1(bwt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
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x = fmt_seed_strategy1(fmt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
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#ifdef SHOW_PERF
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tmp_time = realtime_msec() - tmp_time;
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__sync_fetch_and_add(&time_bwt_smem1a, tmp_time);
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#endif
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if (m.x[2] > 0) kv_push(bwtintv_t, a->mem, m);
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//bwtintv_t *p = &m;
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//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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if (m.x[2] > 0) {
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kv_push(bwtintv_t, a->mem, m);
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//bwtintv_t *p = &m;
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//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
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}
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} else { // for now, we never come to this block which is slower
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x = bwt_smem1a(bwt, len, seq, x, start_width, opt->max_mem_intv, &a->mem1, a->tmpv);
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for (i = 0; i < a->mem1.n; ++i)
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51
fmt_idx.c
51
fmt_idx.c
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@ -855,3 +855,54 @@ fmt_smem_end:
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free(a[0].a);
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return ret;
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}
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int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem)
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{
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int i, kmer_len;
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bwtintv_t ik, ok1, ok2;
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uint64_t qbit;
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memset(mem, 0, sizeof(bwtintv_t));
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if (q[x] > 3)
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return x + 1;
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qbit = (uint32_t)build_forward_kmer(&q[x], len - x, HASH_KMER_LEN, &kmer_len);
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fmt_kmer_get(fmt, &ik, qbit, kmer_len-1); // 初始碱基位置
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ik.info = x + kmer_len;
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#define COND_SET_RETURN(iv, ov, start_pos, end_pos, max_intv, min_len) \
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if (iv.x[2] < max_intv && end_pos - start_pos >= min_len) \
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{ \
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(ov) = (iv); \
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(ov).info = (uint64_t)start_pos << 32 | (end_pos + 1); \
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return end_pos + 1; \
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}
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for (i = (int)ik.info; i + 1 < len; i += 2)
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{ // forward search
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if (q[i] < 4 && q[i + 1] < 4)
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{
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fmt_extend2(fmt, &ik, &ok1, &ok2, 0, 3 - q[i], 3 - q[i + 1]);
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COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
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COND_SET_RETURN(ok2, *mem, x, i + 1, max_intv, min_len);
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ik = ok2;
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}
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else if (q[i] < 4) // q[i+1] >= 4
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{
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fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
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COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
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return i + 2;
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}
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else // q[i] >= 4
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{
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return i + 1;
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}
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}
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if (i == len - 1) {
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fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
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COND_SET_RETURN(ok1, *mem, x, i, max_intv, min_len);
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}
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return len;
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}
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@ -131,4 +131,5 @@ void fmt_kmer_get(const FMTIndex *fmt, bwtintv_t *ok, uint32_t qbit, int pos);
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// 找smem（seed）
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int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
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int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem);
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#endif
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10
run.sh
10
run.sh
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@ -4,16 +4,16 @@ thread=1
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#n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
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#n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
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#reference=~/data/reference/human_g1k_v37_decoy.fasta
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n_r1=~/fastq/sn_r1.fq
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n_r2=~/fastq/sn_r2.fq
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#n_r1=~/fastq/tiny_n_r1.fq
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#n_r2=~/fastq/tiny_n_r3.fq
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#n_r1=~/fastq/sn_r1.fq
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#n_r2=~/fastq/sn_r2.fq
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n_r1=~/fastq/tiny_n_r1.fq
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n_r2=~/fastq/tiny_n_r2.fq
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#n_r1=~/fastq/diff_r1.fq
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#n_r2=~/fastq/diff_r2.fq
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#n_r1=~/fastq/d_r1.fq
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#n_r2=~/fastq/d_r2.fq
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reference=~/reference/human_g1k_v37_decoy.fasta
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out=./fmt_all.sam
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out=./out.sam
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#out=/dev/null
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#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
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