zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

wrong HPC

This commit is contained in:
Heng Li 2017-05-04 17:45:19 +08:00
parent 06adabd0dc
commit 10db6b0434
2 changed files with 6 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
map.c
View File

@ -10,7 +10,7 @@
void mm_mapopt_init(mm_mapopt_t *opt) void mm_mapopt_init(mm_mapopt_t *opt)
{ {
memset(opt, 0, sizeof(mm_mapopt_t)); memset(opt, 0, sizeof(mm_mapopt_t));
opt->n_frag_mini = 100; opt->n_frag_mini = 1000;
opt->max_occ_frac = 1e-5f; opt->max_occ_frac = 1e-5f;
opt->mid_occ_frac = 2e-4f; opt->mid_occ_frac = 2e-4f;
opt->sdust_thres = 0; opt->sdust_thres = 0;
@ -261,7 +261,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
} }
} }
radix_sort_128x(a, a + n_a); radix_sort_128x(a, a + n_a);
// for (i = 0; i < n_a; ++i) printf("%c\t%d\t%d\n", "+-"[a[i].x>>63], (uint32_t)a[i].x>>1, (uint32_t)a[i].y); //for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
t = (int*)kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int)); t = (int*)kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int));
n_t = mm_liss(opt->radius, opt->min_cnt, b->km_fixed, n_a, a, t); n_t = mm_liss(opt->radius, opt->min_cnt, b->km_fixed, n_a, a, t);
@ -278,7 +278,9 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
else if (t[i] > max2) max2 = t[i]; else if (t[i] > max2) max2 = t[i];
off += t[i]; off += t[i];
} }
printf("%s\t%d\t%d\t", qname, max, max2); if (a_st) printf("%s:%d-%d", qname, (uint32_t)a_st->y, (uint32_t)(a_en-1)->y);
else printf("%s:*", qname);
printf("\t%d\t%d\t", max, max2);
if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x>>1, (uint32_t)(a_en-1)->x>>1); if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x>>1, (uint32_t)(a_en-1)->x>>1);
else printf("*"); else printf("*");
printf("\t%d\t%d\t%d\t%d\t%d\n", n_tot, n_low, s_low, n, n_t); printf("\t%d\t%d\t%d\t%d\t%d\n", n_tot, n_low, s_low, n, n_t);

2
sketch.c
View File

@ -112,7 +112,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
info.x = hash64(kmer[z], mask) << 8 | kmer_span; info.x = hash64(kmer[z], mask) << 8 | kmer_span;
info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z; info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z;
} }
} else l = 0, tq.count = tq.front = 0; } else l = 0, tq.count = tq.front = 0, kmer_span = 0;
buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
if (l == w + k - 1) { // special case for the first window - because identical k-mers are not stored yet if (l == w + k - 1) { // special case for the first window - because identical k-mers are not stored yet
for (j = buf_pos + 1; j < w; ++j) for (j = buf_pos + 1; j < w; ++j)