mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-28 17:28:11 +08:00
for break points at chr11
This commit is contained in:
Haoyu Cheng
+649
-33
@@ -537,19 +537,12 @@ int* r_extra_begin, int* r_extra_end, long long* r_y_start, long long* r_y_lengt
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currentIDLen = Get_READ_LENGTH((*R_INF), y_ID);
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///since Window_Len == x_len + (threshold << 1)
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if(currentIDLen <= y_start ||
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if(y_start < 0 || currentIDLen <= y_start ||
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currentIDLen - y_start + 2 * threshold + THRESHOLD_MAX_SIZE < Window_Len)
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{
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return 0;
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}
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/**
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if(currentIDLen <= y_start)
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{
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return 0;
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}
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**/
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extra_begin = extra_end = 0;
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///y maybe less than 0
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y_start = y_start - threshold;
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@@ -1054,6 +1047,71 @@ UC_Read* g_read)
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return T_error;
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}
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inline int double_error_threshold(int pre_threshold, int x_len)
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{
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pre_threshold = Adjust_Threshold(pre_threshold, x_len);
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int threshold = pre_threshold * 2;
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///may have some bugs
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if(x_len >= 300 && threshold < THRESHOLD_MAX_SIZE)
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{
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threshold = THRESHOLD_MAX_SIZE;
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}
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if(threshold > THRESHOLD_MAX_SIZE)
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{
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threshold = THRESHOLD_MAX_SIZE;
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}
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return threshold;
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}
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inline int verify_sub_window(All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read,
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long long x_beg, long long xLen, long long y_beg, long long yLen, uint64_t y_id,
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uint64_t y_pos_strand, int threshold, int alignment_strand,
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unsigned int* get_error, int* get_y_end, int* get_x_end, int* get_aligned_xLen)
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{
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(*get_aligned_xLen) = 0;
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(*get_y_end) = -1;
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(*get_x_end) = -1;
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(*get_error) = (unsigned int)-1;
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int extra_begin, extra_end, r_x_end, r_y_end, aligned_xLen;
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long long o_len;
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unsigned int r_error;
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if(!determine_overlap_region(threshold, y_beg, y_id, yLen,
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R_INF, &extra_begin, &extra_end, &y_beg, &o_len))
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{
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return 0;
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}
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fill_subregion(dumy->overlap_region, y_beg, o_len, y_pos_strand, R_INF,
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y_id, extra_begin, extra_end);
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char* x_string = g_read->seq + x_beg;
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char* y_string = dumy->overlap_region;
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aligned_xLen = 0;
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alignment_extension(y_string, yLen, x_string, xLen, threshold,
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alignment_strand, &r_error, &r_y_end, &r_x_end, &aligned_xLen);
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(*get_error) = r_error;
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(*get_y_end) = r_y_end;
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(*get_x_end) = r_x_end;
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(*get_aligned_xLen) = aligned_xLen;
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if(aligned_xLen == 0)
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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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return 1;
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}
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}
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inline double non_trim_error_rate(overlap_region_alloc* overlap_list, long long ID,
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All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
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{
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@@ -1076,13 +1134,96 @@ All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
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}
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else
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{
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tError +=
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get_high_error(overlap_list->list[ID].w_list[i].x_start,
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overlap_list->list[ID].w_list[i].x_end, overlap_list->list[ID].w_list[i].y_start,
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overlap_list->list[ID].w_list[i].y_end, overlap_list->list[ID].y_id,
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overlap_list->list[ID].y_pos_strand,
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overlap_list->list[ID].w_list[i].error_threshold - overlap_list->list[ID].w_list[i].extra_begin,
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3, 0.3, R_INF, dumy, g_read);
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int x_len = subWinLen;
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int threshold = double_error_threshold(overlap_list->list[ID].w_list[i].error_threshold, x_len);
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int Window_Len = x_len + (threshold << 1);
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unsigned int r_error_left;
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int r_x_end_left, r_y_end_left, aligned_xLen_left;
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unsigned int r_error_right;
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int r_x_end_right, r_y_end_right, aligned_xLen_right;
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long long y_beg_left, y_beg_right;
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aligned_xLen_left = aligned_xLen_right = 0;
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y_beg_left = y_beg_right = -1;
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if(overlap_list->list[ID].w_list[i].y_start == -1)
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{
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tError += x_len;
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continue;
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}
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///if the previous window is mapped
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if(i > 0 && overlap_list->list[ID].w_list[i - 1].y_end != -1)
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{
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y_beg_left = overlap_list->list[ID].w_list[i - 1].y_end + 1;
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}
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///if the next window is mapped
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if(i < overlap_list->list[ID].w_list_length - 1 && overlap_list->list[ID].w_list[i + 1].y_end != -1)
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{
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y_beg_right = 1 + overlap_list->list[ID].w_list[i + 1].y_start - 1 - x_len;
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}
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///cannot apply this strategy to the leftmost and the rightmost window
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if(y_beg_left == -1 && y_beg_right == -1 && i > 0 && i < subWinNum - 1)
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{
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y_beg_left = overlap_list->list[ID].w_list[i].y_start;
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if(overlap_list->list[ID].w_list[i].extra_begin >= 0)
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{
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y_beg_left = y_beg_left + overlap_list->list[ID].w_list[i].error_threshold -
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overlap_list->list[ID].w_list[i].extra_begin;
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}
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y_beg_right = y_beg_left;
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}
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if(y_beg_left != -1)
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{
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verify_sub_window(R_INF, dumy, g_read, overlap_list->list[ID].w_list[i].x_start,
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x_len, y_beg_left, Window_Len, overlap_list->list[ID].y_id, overlap_list->list[ID].y_pos_strand,
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threshold, 0, &r_error_left, &r_y_end_left, &r_x_end_left, &aligned_xLen_left);
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}
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if(y_beg_right != -1)
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{
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verify_sub_window(R_INF, dumy, g_read, overlap_list->list[ID].w_list[i].x_start,
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x_len, y_beg_right, Window_Len, overlap_list->list[ID].y_id, overlap_list->list[ID].y_pos_strand,
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threshold, 1, &r_error_right, &r_y_end_right, &r_x_end_right, &aligned_xLen_right);
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}
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///here one of aligned_xLen_left and aligned_xLen_right must be 0
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if((i == 0 || i == subWinNum - 1) &&
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(x_len - (aligned_xLen_left + aligned_xLen_right) > 10))
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{
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return 1.0;
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}
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///aligned in both direction
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if(aligned_xLen_left != 0 && aligned_xLen_right != 0)
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{
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if(aligned_xLen_left + aligned_xLen_right <= x_len)
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{
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tError = tError + r_error_left + r_error_right +
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(x_len - aligned_xLen_left - aligned_xLen_right);
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}
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else
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{
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float E_rate = (float)(x_len)/(float)(aligned_xLen_left + aligned_xLen_right);
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tError = tError + (r_error_left + r_error_right)*E_rate;
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}
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}///not aligned in both direction
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else if(aligned_xLen_left == 0 && aligned_xLen_right == 0)
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{
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tError += x_len;
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}///only aligned in left
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else if(aligned_xLen_left != 0)
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{
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tError = tError + r_error_left + (x_len - aligned_xLen_left);
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}///only aligned in right
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else if(aligned_xLen_right != 0)
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{
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tError = tError + r_error_right + (x_len - aligned_xLen_right);
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}
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}
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}
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@@ -1912,6 +2053,7 @@ int* r_extra_begin, int* r_extra_end, unsigned int* r_error)
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int path_length;
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///if the start pos at the left boundary
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if(local_y_start == 0)
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{
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total_y_start = total_y_start + local_y_start;
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@@ -2012,24 +2154,7 @@ int* r_extra_begin, int* r_extra_end, unsigned int* r_error)
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}
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inline int double_error_threshold(int pre_threshold, int x_len)
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{
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pre_threshold = Adjust_Threshold(pre_threshold, x_len);
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int threshold = pre_threshold * 2;
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///may have some bugs
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if(x_len >= 300 && threshold < THRESHOLD_MAX_SIZE)
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{
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threshold = THRESHOLD_MAX_SIZE;
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}
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if(threshold > THRESHOLD_MAX_SIZE)
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{
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threshold = THRESHOLD_MAX_SIZE;
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}
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return threshold;
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}
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inline void recalcate_window_back(overlap_region_alloc* overlap_list, All_reads* R_INF,
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@@ -2716,7 +2841,7 @@ inline void recalcate_window_back(overlap_region_alloc* overlap_list, All_reads*
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}
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inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_INF,
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inline void recalcate_window_simple(overlap_region_alloc* overlap_list, All_reads* R_INF,
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UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read)
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{
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long long j, k, i;
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@@ -3275,6 +3400,497 @@ inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_IN
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inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_INF,
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UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read)
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{
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long long j, k, i;
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long long Len_x;
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int threshold;
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long long y_len;
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long long currentIDLen;
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long long matches;
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long long y_id;
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int y_strand;
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long long y_readLen;
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long long x_start;
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long long x_end;
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long long x_len;
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long long total_y_start;
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long long total_y_end;
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long long y_start;
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long long y_end;
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long long Window_Len;
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char* x_string;
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char* y_string;
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int end_site;
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unsigned int error;
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int real_y_start;
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long long overlap_length;
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int extra_begin, extra_end;
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long long o_len;
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///j负责遍历整个overlap list
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for (j = 0; j < overlap_list->length; j++)
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{
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y_id = overlap_list->list[j].y_id;
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y_strand = overlap_list->list[j].y_pos_strand;
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y_readLen = Get_READ_LENGTH((*R_INF), y_id);
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//i corresponding to each window of a overlap
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//utilize the the end pos of pre-window in backwards
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for (i = overlap_list->list[j].w_list_length - 1; i >= 0; i--)
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{
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///the first matched window
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if(overlap_list->list[j].w_list[i].y_end != -1)
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{
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///note!!! need notification
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///this is the actual end postion in ystring
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total_y_start = overlap_list->list[j].w_list[i].y_end
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- overlap_list->list[j].w_list[i].extra_begin + 1;
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///k corresponding to all unmatched windows at the right side of overlap_list->list[j].w_list[i]
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///so k starts from i + 1, and end to the first matched window
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for (k = i + 1; k < overlap_list->list[j].w_list_length && overlap_list->list[j].w_list[k].y_end == -1; k++)
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{
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extra_begin = extra_end = 0;
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///if y_start > y_readLen, direct terminate
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if (total_y_start >= y_readLen)
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{
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break;
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}
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///there is no problem for x
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x_start = overlap_list->list[j].w_list[k].x_start;
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x_end = overlap_list->list[j].w_list[k].x_end;
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x_len = x_end - x_start + 1;
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///there are two potiential reasons for unmatched window:
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///1. this window has a large number of differences
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///2. DP does not start from the right offset
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threshold = double_error_threshold(overlap_list->list[j].w_list[k].error_threshold, x_len);
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y_start = total_y_start;
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Window_Len = x_len + (threshold << 1);
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if(!determine_overlap_region(threshold, y_start, y_id, Window_Len, R_INF,
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&extra_begin, &extra_end, &y_start, &o_len))
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{
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break;
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}
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if(o_len + threshold < x_len)
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{
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break;
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}
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fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
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R_INF, y_id, extra_begin, extra_end);
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x_string = g_read->seq + x_start;
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y_string = dumy->overlap_region;
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///note!!! need notification
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end_site = Reserve_Banded_BPM(y_string, Window_Len, x_string, x_len, threshold, &error);
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// unsigned int debug_error;
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// int return_y_end, return_x_end;
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// Reserve_Banded_BPM_Extension(y_string, Window_Len, x_string, x_len, threshold,
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// &debug_error, &return_y_end, &return_x_end);
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// if(return_x_end != x_len - 1 && end_site != -1)
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// {
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// fprintf(stderr, "error\n");
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// }
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// if(return_x_end == x_len - 1 && end_site == -1)
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// {
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// fprintf(stderr, "error\n");
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// }
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// if(return_x_end == x_len - 1 && end_site != -1)
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// {
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// if(return_y_end != end_site || debug_error != error)
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// {
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// fprintf(stderr, "error\n");
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// }
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// }
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///error等于-1说明没匹配
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if (error!=(unsigned int)-1)
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{
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overlap_list->list[j].w_list[k].cigar.length = -1;
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overlap_list->list[j].w_list[k].y_start = y_start;
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overlap_list->list[j].w_list[k].y_end = y_start + end_site;
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overlap_list->list[j].w_list[k].error = (int)error;
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///note!!! need notification
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||||
overlap_list->list[j].w_list[k].extra_begin = extra_begin;
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overlap_list->list[j].w_list[k].extra_end = extra_end;
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overlap_list->list[j].w_list[k].error_threshold = threshold;
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||||
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overlap_list->list[j].align_length += x_len;
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}
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||||
else
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||||
{
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||||
break;
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||||
}
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||||
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||||
///note!!! need notification
|
||||
total_y_start = y_start + end_site - extra_begin + 1;
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||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
//i corresponding to each window of a overlap
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||||
//utilize the the start pos of next window in forward
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||||
for (i = 0; i < overlap_list->list[j].w_list_length; i++)
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||||
{
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||||
///find the first matched window, which should not be the first window
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||||
///the pre-window of this matched window must be unmatched
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||||
if(overlap_list->list[j].w_list[i].y_end != -1 && i != 0 && overlap_list->list[j].w_list[i - 1].y_end == -1)
|
||||
{
|
||||
///check if the start pos of this matched window has been calculated
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||||
if(overlap_list->list[j].w_list[i].cigar.length == -1)
|
||||
{
|
||||
///there is no problem for x
|
||||
x_start = overlap_list->list[j].w_list[i].x_start;
|
||||
x_end = overlap_list->list[j].w_list[i].x_end;
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x_len = x_end - x_start + 1;
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||||
/****************************may have bugs********************************/
|
||||
threshold = overlap_list->list[j].w_list[i].error_threshold;
|
||||
/****************************may have bugs********************************/
|
||||
/****************************may have bugs********************************/
|
||||
///should not adjust threshold, since this window can be matched by the old threshold
|
||||
///threshold = Adjust_Threshold(threshold, x_len);
|
||||
/****************************may have bugs********************************/
|
||||
Window_Len = x_len + (threshold << 1);
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||||
|
||||
|
||||
///y_start is the real y_start
|
||||
y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
extra_begin = overlap_list->list[j].w_list[i].extra_begin;
|
||||
extra_end = overlap_list->list[j].w_list[i].extra_end;
|
||||
o_len = Window_Len - extra_end - extra_begin;
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path,
|
||||
overlap_list->list[j].w_list[i].error, overlap_list->list[j].w_list[i].y_end - y_start);
|
||||
|
||||
|
||||
///y_start has already been calculated
|
||||
if (error != (unsigned int)-1)
|
||||
{
|
||||
///this condition is always wrong
|
||||
///in best case, real_y_start = threshold, end_site = Window_Len - threshold - 1
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
if(fix_boundary(x_string, x_len, threshold, y_start, real_y_start,
|
||||
end_site, extra_begin, extra_end, y_id, Window_Len, R_INF, dumy,
|
||||
y_strand, error, &y_start, &real_y_start, &end_site, &extra_begin,
|
||||
&extra_end, &error))
|
||||
{
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
overlap_list->list[j].w_list[i].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[i].extra_end = extra_end;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[i]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
// if(real_y_start < extra_begin || end_site >= Window_Len - extra_end)
|
||||
// {
|
||||
// fprintf(stderr, "\nreal_y_start: %d, extra_begin: %d\n",
|
||||
// real_y_start, extra_begin);
|
||||
|
||||
// fprintf(stderr, "end_site: %d, Window_Len: %d, extra_end: %d\n",
|
||||
// end_site, Window_Len, extra_end);
|
||||
// }
|
||||
|
||||
|
||||
///note!!! need notification
|
||||
real_y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[i].y_start = real_y_start;
|
||||
///I forget why don't reduce the extra_begin for y_end
|
||||
///it seems extra_begin will be reduced at the end of this function
|
||||
overlap_list->list[j].w_list[i].y_end = y_start + end_site;
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
}
|
||||
else
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
real_y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
}
|
||||
|
||||
|
||||
|
||||
///the end pos for pre window is real_y_start - 1
|
||||
total_y_end = real_y_start - 1;
|
||||
///k遍历匹配window左侧所有不匹配的window
|
||||
///如果i匹配，则k从i-1开始
|
||||
///直到第一个匹配的window结束
|
||||
///因为i!=0，所以k的大小不用担心
|
||||
for (k = i - 1; k >= 0 && overlap_list->list[j].w_list[k].y_end == -1; k--)
|
||||
{
|
||||
///there is no problem in x
|
||||
x_start = overlap_list->list[j].w_list[k].x_start;
|
||||
x_end = overlap_list->list[j].w_list[k].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
///there are two potiential reasons for unmatched window:
|
||||
///1. this window has a large number of differences
|
||||
///2. DP does not start from the right offset
|
||||
threshold = double_error_threshold(overlap_list->list[j].w_list[k].error_threshold, x_len);
|
||||
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
if(total_y_end <= 0)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
///y_start might be less than 0
|
||||
y_start = total_y_end - x_len + 1;
|
||||
if(!determine_overlap_region(threshold, y_start, y_id, Window_Len, R_INF,
|
||||
&extra_begin, &extra_end, &y_start, &o_len))
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
if(o_len + threshold < x_len)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path, -1, -1);
|
||||
|
||||
if (error!=(unsigned int)-1)
|
||||
{
|
||||
///this condition is always wrong
|
||||
///in best case, real_y_start = threshold, end_site = Window_Len - threshold - 1
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
fix_boundary(x_string, x_len, threshold, y_start, real_y_start, end_site,
|
||||
extra_begin, extra_end, y_id, Window_Len, R_INF, dumy, y_strand, error,
|
||||
&y_start, &real_y_start, &end_site,
|
||||
&extra_begin, &extra_end, &error);
|
||||
}
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[k]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
// if(real_y_start < extra_begin || end_site >= Window_Len - extra_end)
|
||||
// {
|
||||
// fprintf(stderr, "\nreal_y_start: %d, extra_begin: %d\n",
|
||||
// real_y_start, extra_begin);
|
||||
|
||||
// fprintf(stderr, "end_site: %d, Window_Len: %d, extra_end: %d\n",
|
||||
// end_site, Window_Len, extra_end);
|
||||
// }
|
||||
|
||||
///y_start has no shift, but y_end has shift
|
||||
overlap_list->list[j].w_list[k].y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[k].y_end = y_start + end_site;
|
||||
overlap_list->list[j].w_list[k].error = error;
|
||||
overlap_list->list[j].align_length += x_len;
|
||||
overlap_list->list[j].w_list[k].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[k].extra_end = extra_end;
|
||||
overlap_list->list[j].w_list[k].error_threshold = threshold;
|
||||
}
|
||||
else
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
total_y_end = y_start + real_y_start - 1 - extra_begin;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
overlap_list->mapped_overlaps_length = 0;
|
||||
|
||||
int pre_threshold;
|
||||
long long tLen, tError;
|
||||
double error_rate;
|
||||
for (j = 0; j < overlap_list->length; j++)
|
||||
{
|
||||
y_id = overlap_list->list[j].y_id;
|
||||
y_strand = overlap_list->list[j].y_pos_strand;
|
||||
y_readLen = Get_READ_LENGTH((*R_INF), y_id);
|
||||
overlap_length = overlap_list->list[j].x_pos_e - overlap_list->list[j].x_pos_s + 1;
|
||||
overlap_list->list[j].is_match = 0;
|
||||
|
||||
|
||||
///only calculate cigar for high quality overlaps
|
||||
if (overlap_length * OVERLAP_THRESHOLD_FILTER <= overlap_list->list[j].align_length)
|
||||
{
|
||||
|
||||
for (i = 0; i < overlap_list->list[j].w_list_length; i++)
|
||||
{
|
||||
///first we need to check if this window is matched
|
||||
if(overlap_list->list[j].w_list[i].y_end != -1)
|
||||
{
|
||||
///second check if the cigar of this window has been got
|
||||
if(overlap_list->list[j].w_list[i].cigar.length == -1)
|
||||
{
|
||||
///there is no problem for x
|
||||
x_start = overlap_list->list[j].w_list[i].x_start;
|
||||
x_end = overlap_list->list[j].w_list[i].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
/****************************may have bugs********************************/
|
||||
///threshold = x_len * THRESHOLD_RATE;
|
||||
threshold = overlap_list->list[j].w_list[i].error_threshold;
|
||||
/****************************may have bugs********************************/
|
||||
/****************************may have bugs********************************/
|
||||
///should not adjust threshold, since this window can be matched by the old threshold
|
||||
///threshold = Adjust_Threshold(threshold, x_len);
|
||||
/****************************may have bugs********************************/
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
|
||||
///y_start is the real y_start
|
||||
///for the window with cigar, y_start has already reduced extra_begin
|
||||
y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
extra_begin = overlap_list->list[j].w_list[i].extra_begin;
|
||||
extra_end = overlap_list->list[j].w_list[i].extra_end;
|
||||
o_len = Window_Len - extra_end - extra_begin;
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path,
|
||||
overlap_list->list[j].w_list[i].error, overlap_list->list[j].w_list[i].y_end - y_start);
|
||||
|
||||
// if(error != overlap_list->list[j].w_list[i].error)
|
||||
// {
|
||||
// fprintf(stderr, "error\n");
|
||||
// }
|
||||
|
||||
if (error != (unsigned int)-1)
|
||||
{
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
|
||||
if(fix_boundary(x_string, x_len, threshold, y_start, real_y_start, end_site,
|
||||
extra_begin, extra_end, y_id, Window_Len, R_INF, dumy, y_strand, error,
|
||||
&y_start, &real_y_start, &end_site,
|
||||
&extra_begin, &extra_end, &error))
|
||||
{
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
overlap_list->list[j].w_list[i].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[i].extra_end = extra_end;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[i]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
|
||||
// if(real_y_start < extra_begin || end_site >= Window_Len - extra_end)
|
||||
// {
|
||||
// fprintf(stderr, "\nreal_y_start: %d, extra_begin: %d\n",
|
||||
// real_y_start, extra_begin);
|
||||
|
||||
// fprintf(stderr, "end_site: %d, Window_Len: %d, extra_end: %d\n",
|
||||
// end_site, Window_Len, extra_end);
|
||||
// }
|
||||
|
||||
///note!!! need notification
|
||||
real_y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[i].y_start = real_y_start;
|
||||
overlap_list->list[j].w_list[i].y_end = y_start + end_site - extra_begin;
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
}
|
||||
else
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
overlap_list->list[j].w_list[i].y_end -= overlap_list->list[j].w_list[i].extra_begin;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
///error_rate = trim_error_rate(overlap_list, j);
|
||||
error_rate = non_trim_error_rate(overlap_list, j, R_INF, dumy, g_read);
|
||||
|
||||
|
||||
///if(error_rate <= 0.015)
|
||||
if(error_rate <= 0.03)
|
||||
{
|
||||
overlap_list->mapped_overlaps_length += overlap_length;
|
||||
overlap_list->list[j].is_match = 1;
|
||||
}
|
||||
else if(error_rate <= 0.045)
|
||||
{
|
||||
overlap_list->list[j].is_match = 3;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
inline void adjust_alignment_windows(overlap_region* overlap, All_reads* R_INF)
|
||||
{
|
||||
long long y_id = overlap->y_id;
|
||||
long long y_strand = overlap->y_pos_strand;
|
||||
long long y_readLen = Get_READ_LENGTH((*R_INF), y_id);
|
||||
long long overlap_length = overlap->x_pos_e - overlap->x_pos_s + 1;
|
||||
long long i;
|
||||
///note here we start from i = 1, instead of i = 0
|
||||
for (i = 1; i < overlap->w_list_length; i++)
|
||||
{
|
||||
///that means we have both start pos and end pos
|
||||
if(overlap->w_list[i].y_end != -1 && overlap->w_list[i].cigar.length != -1)
|
||||
{
|
||||
;
|
||||
}
|
||||
}
|
||||
}
|
||||
**/
|
||||
|
||||
|
||||
|
||||
inline void add_base_to_correct_read_directly(Correct_dumy* dumy, char base)
|
||||
{
|
||||
|
||||
|
||||
Reference in New Issue
Block a user