mirror of
https://github.com/chhylp123/hifiasm.git
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for break points at chr11
This commit is contained in:
Haoyu Cheng
+381
-79
@@ -632,6 +632,225 @@ void append_overlap_region_alloc_from_existing(overlap_region_alloc* list, overl
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}
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int append_inexact_overlap_region_alloc_back(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF)
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{
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if (list->length + 1 > list->size)
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{
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list->size = list->size * 2;
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list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
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///新分配空间要初始化
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memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
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}
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if (list->length!=0 &&
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list->list[list->length - 1].y_id==tmp->y_id
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)
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{
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if(list->list[list->length - 1].shared_seed >= tmp->shared_seed)
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{
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return 0;
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}
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else
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{
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list->length--;
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}
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}
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if(tmp->x_pos_s <= tmp->y_pos_s)
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{
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tmp->y_pos_s = tmp->y_pos_s - tmp->x_pos_s;
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tmp->x_pos_s = 0;
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}
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else
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{
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tmp->x_pos_s = tmp->x_pos_s - tmp->y_pos_s;
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tmp->y_pos_s = 0;
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}
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long long x_right_length = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
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long long y_right_length = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
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if(x_right_length <= y_right_length)
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{
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tmp->x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - 1;
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tmp->y_pos_e = tmp->y_pos_e + x_right_length;
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}
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else
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{
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tmp->x_pos_e = tmp->x_pos_e + y_right_length;
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tmp->y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - 1;
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}
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if (tmp->x_pos_strand == 1)
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{
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list->list[list->length].x_id = tmp->x_id;
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list->list[list->length].x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
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list->list[list->length].x_pos_s = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
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list->list[list->length].x_pos_strand = 0;
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list->list[list->length].y_id = tmp->y_id;
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list->list[list->length].y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
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list->list[list->length].y_pos_s = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
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list->list[list->length].y_pos_strand = 1;
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resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
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add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
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long long distance_gap;
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long long pre_distance_gap = 0;
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long long i = 0;
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for (i = 0; i < tmp->f_cigar.length; i++)
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{
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distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
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if(distance_gap != pre_distance_gap)
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{
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pre_distance_gap = distance_gap;
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add_fake_cigar(&(list->list[list->length].f_cigar),
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Get_READ_LENGTH((*R_INF), tmp->x_id) - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
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pre_distance_gap);
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}
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}
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if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
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list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
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{
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add_fake_cigar(&(list->list[list->length].f_cigar),
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list->list[list->length].x_pos_e,
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get_fake_gap_shift(&(list->list[list->length].f_cigar),
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list->list[list->length].f_cigar.length - 1));
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}
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/******************************for debug********************************/
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// long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
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// long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
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// distance_gap = distance_pos - distance_self_pos;
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// if(distance_gap !=
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// get_fake_gap_shift(&(list->list[list->length].f_cigar),
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// list->list[list->length].f_cigar.length - 1))
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// {
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// fprintf(stderr, "error\n");
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// }
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// long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
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// long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
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// distance_gap = distance_pos - distance_self_pos;
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// fprintf(stderr, "\nx_s: %d, x_e: %d, y_s: %d, y_e: %d, distance_gap: %d, xLen: %d\n",
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// list->list[list->length].x_pos_s, list->list[list->length].x_pos_e,
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// list->list[list->length].y_pos_s, list->list[list->length].y_pos_e, distance_gap,
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// Get_READ_LENGTH((*R_INF), tmp->x_id));
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// for (i = 0; i < list->list[list->length].f_cigar.length; i++)
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// {
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// fprintf(stderr, "##i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
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// i, get_fake_gap_pos(&(list->list[list->length].f_cigar), i),
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// get_fake_gap_shift(&(list->list[list->length].f_cigar), i));
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// }
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// for (i = 0; i < tmp->f_cigar.length; i++)
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// {
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// fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
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// i, get_fake_gap_pos(&(tmp->f_cigar), i),
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// get_fake_gap_shift(&(tmp->f_cigar), i));
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// }
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/******************************for debug********************************/
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}
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else
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{
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list->list[list->length].x_id = tmp->x_id;
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list->list[list->length].x_pos_e = tmp->x_pos_e;
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list->list[list->length].x_pos_s = tmp->x_pos_s;
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list->list[list->length].x_pos_strand = tmp->x_pos_strand;
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list->list[list->length].y_id = tmp->y_id;
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list->list[list->length].y_pos_e = tmp->y_pos_e;
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list->list[list->length].y_pos_s = tmp->y_pos_s;
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list->list[list->length].y_pos_strand = tmp->y_pos_strand;
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resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
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add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
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long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
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long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
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long long init_distance_gap = distance_pos - distance_self_pos;
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long long pre_distance_gap = init_distance_gap;
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long long distance_gap;
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long long i = 0;
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for (i = tmp->f_cigar.length - 1; i >= 0; i--)
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{
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distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
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if(distance_gap != pre_distance_gap)
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{
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pre_distance_gap = distance_gap;
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add_fake_cigar(&(list->list[list->length].f_cigar),
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get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap);
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}
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}
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if(get_fake_gap_pos(&(list->list[list->length].f_cigar),
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list->list[list->length].f_cigar.length - 1) != list->list[list->length].x_pos_e)
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{
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add_fake_cigar(&(list->list[list->length].f_cigar),
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list->list[list->length].x_pos_e,
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get_fake_gap_shift(&(list->list[list->length].f_cigar),
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list->list[list->length].f_cigar.length - 1));
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}
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/******************************for debug********************************/
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// distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
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// distance_pos = tmp->y_pos_e - tmp->y_pos_s;
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// distance_gap = distance_pos - distance_self_pos;
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// if(distance_gap !=
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// get_fake_gap_shift(&(list->list[list->length].f_cigar),
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// list->list[list->length].f_cigar.length - 1))
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// {
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// fprintf(stderr, "error\n");
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// }
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// distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
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// distance_pos = tmp->y_pos_e - tmp->y_pos_s;
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// distance_gap = distance_pos - distance_self_pos;
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// fprintf(stderr, "\nx_s: %d, x_e: %d, y_s: %d, y_e: %d, distance_gap: %d\n",
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// list->list[list->length].x_pos_s, list->list[list->length].x_pos_e,
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// list->list[list->length].y_pos_s, list->list[list->length].y_pos_e, distance_gap);
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// for (i = 0; i < list->list[list->length].f_cigar.length; i++)
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// {
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// fprintf(stderr, "##i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
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// i, get_fake_gap_pos(&(list->list[list->length].f_cigar), i),
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// get_fake_gap_shift(&(list->list[list->length].f_cigar), i));
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// }
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// for (i = 0; i < tmp->f_cigar.length; i++)
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// {
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// fprintf(stderr, "**i: %d, gap_pos_in_x: %d, gap_shift: %d\n",
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// i, get_fake_gap_pos(&(tmp->f_cigar), i),
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// get_fake_gap_shift(&(tmp->f_cigar), i));
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// }
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/******************************for debug********************************/
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}
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list->list[list->length].shared_seed = tmp->shared_seed;
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list->list[list->length].align_length = 0;
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list->list[list->length].is_match = 0;
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list->list[list->length].non_homopolymer_errors = 0;
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list->list[list->length].strong = 0;
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list->length++;
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return 1;
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}
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int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF)
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{
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@@ -1278,6 +1497,164 @@ long long y_beg, long long y_end, long long yLen)
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return x_end - x_beg + 1;
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}
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void chain_DP_back(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
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double band_width_threshold)
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{
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long long i, j;
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long long self_pos, pos, max_j, max_i, max_score, score, n_skip;
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long long distance_pos, distance_self_pos, distance_gap, log_distance_gap, distance_min;
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///double band_width_threshold = 0.05;
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double band_width_penalty = 1 / band_width_threshold;
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long long min_score = k_mer_length;
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long long max_indels, max_self_length;
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double gap_rate;
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long long total_indels, total_self_length;
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resize_Chain_Data(dp, a_n);
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// fill the score and backtrack arrays
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for (i = 0; i < a_n; ++i)
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{
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pos = a[i].offset;
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self_pos = a[i].self_offset;
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max_j = -1;
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max_score = min_score;
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n_skip = 0;
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max_indels = 0;
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max_self_length = 0;
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///may have a pre-cut condition for j
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for (j = i - 1; j >= 0; --j)
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{
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distance_pos = pos - a[j].offset;
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distance_self_pos = self_pos - a[j].self_offset;
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///a has been sorted by a[].offset
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///note for a, we do not have any two elements that have both equal offsets and self_offsets
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///but there maybe two elements that have equal offsets or equal self_offsets
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if(distance_pos == 0 || distance_self_pos <= 0)
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{
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continue;
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}
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distance_gap = distance_pos > distance_self_pos? distance_pos - distance_self_pos : distance_self_pos - distance_pos;
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total_indels = dp->indels[j] + distance_gap;
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total_self_length = dp->self_length[j] + distance_self_pos;
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if(total_indels > band_width_threshold * total_self_length)
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{
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continue;
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}
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distance_min = distance_pos < distance_self_pos? distance_pos:distance_self_pos;
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score = distance_min < min_score? distance_min : min_score;
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/**
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log_distance_gap = distance_gap? ilog2_32(distance_gap) : 0;
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score -= (long long)(distance_gap * 0.01 * min_score) + (log_distance_gap/2);
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**/
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gap_rate = (double)((double)(total_indels)/(double)(total_self_length));
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///if the gap rate > 0.05, score will be negative
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score -= (long long)(gap_rate * score * band_width_penalty);
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score += dp->score[j];
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if(score > max_score)
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{
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max_score = score;
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max_j = j;
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max_indels = total_indels;
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max_self_length = total_self_length;
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if (n_skip > 0)
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{
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n_skip--;
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}
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}
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}
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dp->score[i] = max_score;
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dp->pre[i] = max_j;
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dp->indels[i] = max_indels;
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dp->self_length[i] = max_self_length;
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}
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///debug_chain(a, a_n, dp);
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max_score = -1;
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max_i = -1;
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for (i = 0; i < a_n; ++i)
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{
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if(dp->score[i] > max_score)
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{
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max_score = dp->score[i];
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max_i = i;
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}
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}
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clear_fake_cigar(&(result->f_cigar));
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i = max_i;
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result->x_pos_e = a[i].self_offset;
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result->y_pos_e = a[i].offset;
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result->shared_seed = max_score;
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distance_self_pos = result->x_pos_e - a[i].self_offset;
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distance_pos = result->y_pos_e - a[i].offset;
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long long pre_distance_gap = distance_pos - distance_self_pos;
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///record first site
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///the length of f_cigar should be at least 1
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add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
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long long chainLen = 0;
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if(result->x_pos_strand == 1)
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{
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while (i >= 0)
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{
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distance_self_pos = result->x_pos_e - a[i].self_offset;
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distance_pos = result->y_pos_e - a[i].offset;
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distance_gap = distance_pos - distance_self_pos;
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if(distance_gap != pre_distance_gap)
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{
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pre_distance_gap = distance_gap;
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///record this site
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add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
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}
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chainLen++;
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result->x_pos_s = a[i].self_offset;
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result->y_pos_s = a[i].offset;
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i = dp->pre[i];
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}
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}
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else
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{
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while (i >= 0)
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{
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distance_self_pos = result->x_pos_e - a[i].self_offset;
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distance_pos = result->y_pos_e - a[i].offset;
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distance_gap = distance_pos - distance_self_pos;
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if(distance_gap == pre_distance_gap)
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{
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result->f_cigar.length--;
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add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
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}
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else
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{
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pre_distance_gap = distance_gap;
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add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
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}
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chainLen++;
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result->x_pos_s = a[i].self_offset;
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result->y_pos_s = a[i].offset;
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i = dp->pre[i];
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}
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}
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}
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///double band_width_threshold = 0.05;
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void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
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double band_width_threshold, int max_skip, int x_readLen, int y_readLen)
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@@ -1618,95 +1995,20 @@ uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_thresh
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continue;
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}
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// if(
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// ((memcmp("m64016_190918_162737/130811282/ccs",
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// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
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// &&
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// (memcmp("m64016_190918_162737/179635219/ccs",
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// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0))
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||||
// ||
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||||
// ((memcmp("m64016_190918_162737/179635219/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
|
||||
// &&
|
||||
// (memcmp("m64016_190918_162737/130811282/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0)))
|
||||
// {
|
||||
// fprintf(stderr, "****************x_name: %.*s****************\n",
|
||||
// Get_NAME_LENGTH((*R_INF), tmp_region.x_id), Get_NAME((*R_INF), tmp_region.x_id));
|
||||
// fprintf(stderr, "****************y_name: %.*s****************\n",
|
||||
// Get_NAME_LENGTH((*R_INF), tmp_region.y_id), Get_NAME((*R_INF), tmp_region.y_id));
|
||||
|
||||
|
||||
// k_mer_hit* k_list = candidates->list + sub_region_beg;
|
||||
// long long k_listLen = sub_region_end - sub_region_beg + 1;
|
||||
// long long k = 0;
|
||||
|
||||
// fprintf(stderr, "k_listLen: %d\n", k_listLen);
|
||||
|
||||
// for (k = 0; k < k_listLen; k++)
|
||||
// {
|
||||
// fprintf(stderr, "k: %d, readID: %d, strand: %d, offset: %d, self_offset: %d\n",
|
||||
// k, k_list[k].readID, k_list[k].strand, k_list[k].offset, k_list[k].self_offset);
|
||||
// }
|
||||
// }
|
||||
|
||||
|
||||
|
||||
chain_DP(candidates->list + sub_region_beg,
|
||||
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), &tmp_region, band_width_threshold,
|
||||
50, Get_READ_LENGTH((*R_INF), tmp_region.x_id), Get_READ_LENGTH((*R_INF), tmp_region.y_id));
|
||||
|
||||
// chain_DP_back(candidates->list + sub_region_beg,
|
||||
// sub_region_end - sub_region_beg + 1, &(candidates->chainDP), &tmp_region, band_width_threshold);
|
||||
|
||||
// if(
|
||||
// ((memcmp("m64016_190918_162737/130811282/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
|
||||
// &&
|
||||
// (memcmp("m64016_190918_162737/179635219/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0))
|
||||
// ||
|
||||
// ((memcmp("m64016_190918_162737/179635219/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.x_id), Get_NAME_LENGTH((*R_INF), tmp_region.x_id)) == 0)
|
||||
// &&
|
||||
// (memcmp("m64016_190918_162737/130811282/ccs",
|
||||
// Get_NAME((*R_INF), tmp_region.y_id), Get_NAME_LENGTH((*R_INF), tmp_region.y_id)) == 0)))
|
||||
// {
|
||||
// fprintf(stderr, "****************x_name: %.*s****************\n",
|
||||
// Get_NAME_LENGTH((*R_INF), tmp_region.x_id), Get_NAME((*R_INF), tmp_region.x_id));
|
||||
// fprintf(stderr, "****************y_name: %.*s****************\n",
|
||||
// Get_NAME_LENGTH((*R_INF), tmp_region.y_id), Get_NAME((*R_INF), tmp_region.y_id));
|
||||
|
||||
|
||||
// k_mer_hit* k_list = candidates->list + sub_region_beg;
|
||||
// long long k_listLen = sub_region_end - sub_region_beg + 1;
|
||||
// long long k = 0;
|
||||
|
||||
// fprintf(stderr, "k_listLen: %d\n", k_listLen);
|
||||
|
||||
// for (k = 0; k < k_listLen; k++)
|
||||
// {
|
||||
// fprintf(stderr, "k: %d, score: %d, pre: %d, indels: %d, self_length: %d\n",
|
||||
// k, candidates->chainDP.score[k], candidates->chainDP.pre[k],
|
||||
// candidates->chainDP.indels[k], candidates->chainDP.self_length[k]);
|
||||
// }
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
||||
///自己和自己重叠的要排除
|
||||
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
|
||||
if (tmp_region.x_id != tmp_region.y_id)
|
||||
{
|
||||
///append_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
|
||||
/**
|
||||
if(append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF))
|
||||
{
|
||||
debug_seed_offset(candidates->list + sub_region_beg,
|
||||
sub_region_end - sub_region_beg + 1,
|
||||
&(candidates->chainDP), &(overlap_list->list[overlap_list->length - 1]), R_INF);
|
||||
}
|
||||
**/
|
||||
append_inexact_overlap_region_alloc(overlap_list, &tmp_region, R_INF);
|
||||
///append_inexact_overlap_region_alloc_back(overlap_list, &tmp_region, R_INF);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user