mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
backup
This commit is contained in:
chhylp123
287
Correct.cpp
287
Correct.cpp
@@ -539,6 +539,236 @@ char* r_string)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void verify_ul_window(long long window_start, long long window_end, overlap_region_alloc* overlap_list,Correct_dumy* dumy, const ma_ug_t *uref,
|
||||
char* r_string)
|
||||
{
|
||||
long long i;
|
||||
long long currentID;
|
||||
long long x_start, y_start, o_len;
|
||||
long long Window_Len = WINDOW + (THRESHOLD << 1);
|
||||
char* x_string = NULL;
|
||||
char* y_string = NULL;
|
||||
long long x_end, x_len;
|
||||
int end_site;
|
||||
unsigned int error;
|
||||
int groupLen = 0;
|
||||
int return_sites[GROUP_SIZE];
|
||||
unsigned int return_sites_error[GROUP_SIZE];
|
||||
uint64_t overlapID[GROUP_SIZE];
|
||||
uint64_t y_startGroup[GROUP_SIZE];
|
||||
int y_extra_begin[GROUP_SIZE];
|
||||
int y_extra_end[GROUP_SIZE];
|
||||
int error_threshold[GROUP_SIZE];
|
||||
int extra_begin;
|
||||
int extra_end;
|
||||
|
||||
///here are overlaps fully covered by WINDOW
|
||||
for (i = 0; i < (long long)dumy->length; i++)
|
||||
{
|
||||
extra_begin = extra_end = 0;
|
||||
///if the window has been fully covered, the interval at x is [window_start, window_end]
|
||||
x_len = WINDOW;
|
||||
currentID = dumy->overlapID[i];
|
||||
x_start = window_start;
|
||||
///offset of y
|
||||
y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;
|
||||
/****************************may have bugs********************************/
|
||||
y_start += y_start_offset(x_start, &(overlap_list->list[currentID].f_cigar));
|
||||
/****************************may have bugs********************************/
|
||||
|
||||
|
||||
if(!determine_overlap_region(THRESHOLD, y_start, overlap_list->list[currentID].y_id, Window_Len, R_INF,
|
||||
&extra_begin, &extra_end, &y_start, &o_len))
|
||||
{
|
||||
append_window_list(&overlap_list->list[currentID], window_start, window_end,
|
||||
-1, -1, -1, -1, -1, -1);
|
||||
continue;
|
||||
}
|
||||
|
||||
fill_subregion(dumy->overlap_region_group[groupLen], y_start, o_len, overlap_list->list[currentID].y_pos_strand,
|
||||
R_INF, overlap_list->list[currentID].y_id, extra_begin, extra_end);
|
||||
|
||||
y_extra_begin[groupLen] = extra_begin;
|
||||
y_extra_end[groupLen] = extra_end;
|
||||
overlapID[groupLen] = currentID;
|
||||
y_startGroup[groupLen] = y_start;
|
||||
error_threshold[groupLen] = THRESHOLD;
|
||||
x_string = r_string + x_start;
|
||||
groupLen++;
|
||||
|
||||
|
||||
if (groupLen == GROUP_SIZE)
|
||||
{
|
||||
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
|
||||
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
|
||||
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
|
||||
groupLen = 0;
|
||||
|
||||
|
||||
if (return_sites_error[0]!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[0]].align_length += x_len;
|
||||
|
||||
append_window_list(&overlap_list->list[overlapID[0]], window_start, window_end,
|
||||
y_startGroup[0], y_startGroup[0] + return_sites[0], (int)return_sites_error[0],
|
||||
y_extra_begin[0], y_extra_end[0], error_threshold[0]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[0]], window_start, window_end, y_startGroup[0], -1, -1,
|
||||
y_extra_begin[0], y_extra_end[0], error_threshold[0]);
|
||||
}
|
||||
|
||||
|
||||
if (return_sites_error[1]!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[1]].align_length += x_len;
|
||||
|
||||
append_window_list(&overlap_list->list[overlapID[1]], window_start, window_end,
|
||||
y_startGroup[1], y_startGroup[1] + return_sites[1], (int)return_sites_error[1],
|
||||
y_extra_begin[1], y_extra_end[1], error_threshold[1]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[1]], window_start, window_end, y_startGroup[1], -1, -1,
|
||||
y_extra_begin[1], y_extra_end[1], error_threshold[1]);
|
||||
}
|
||||
|
||||
|
||||
if (return_sites_error[2]!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[2]].align_length += x_len;
|
||||
|
||||
append_window_list(&overlap_list->list[overlapID[2]], window_start, window_end,
|
||||
y_startGroup[2], y_startGroup[2] + return_sites[2], (int)return_sites_error[2],
|
||||
y_extra_begin[2], y_extra_end[2], error_threshold[2]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[2]], window_start, window_end, y_startGroup[2], -1, -1,
|
||||
y_extra_begin[2], y_extra_end[2], error_threshold[2]);
|
||||
}
|
||||
|
||||
|
||||
if (return_sites_error[3]!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[3]].align_length += x_len;
|
||||
|
||||
append_window_list(&overlap_list->list[overlapID[3]], window_start, window_end,
|
||||
y_startGroup[3], y_startGroup[3] + return_sites[3], (int)return_sites_error[3],
|
||||
y_extra_begin[3], y_extra_end[3], error_threshold[3]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[3]], window_start, window_end, y_startGroup[3], -1, -1,
|
||||
y_extra_begin[3], y_extra_end[3], error_threshold[3]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (groupLen == 1)
|
||||
{
|
||||
end_site = Reserve_Banded_BPM(dumy->overlap_region_group[0], Window_Len, x_string, WINDOW, THRESHOLD, &error);
|
||||
|
||||
if (error!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[0]].align_length += x_len;
|
||||
|
||||
append_window_list(&overlap_list->list[overlapID[0]], window_start, window_end,
|
||||
y_startGroup[0], y_startGroup[0] + end_site, (int)error,
|
||||
y_extra_begin[0], y_extra_end[0], error_threshold[0]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[0]], window_start, window_end, y_startGroup[0], -1, -1,
|
||||
y_extra_begin[0], y_extra_end[0], error_threshold[0]);
|
||||
}
|
||||
}
|
||||
else if (groupLen > 1)
|
||||
{
|
||||
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
|
||||
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
|
||||
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
|
||||
|
||||
for (i = 0; i < groupLen; i++)
|
||||
{
|
||||
if (return_sites_error[i]!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[overlapID[i]].align_length += x_len;
|
||||
append_window_list(&overlap_list->list[overlapID[i]], window_start, window_end,
|
||||
y_startGroup[i], y_startGroup[i] + return_sites[i], (int)return_sites_error[i],
|
||||
y_extra_begin[i], y_extra_end[i], error_threshold[i]);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[overlapID[i]], window_start, window_end, y_startGroup[i], -1, -1,
|
||||
y_extra_begin[i], y_extra_end[i], error_threshold[i]);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
groupLen = 0;
|
||||
}
|
||||
|
||||
long long reverse_i = dumy->size - 1;
|
||||
int threshold;
|
||||
|
||||
///here are overlaps partially covered by WINDOW
|
||||
for (i = 0; i < (long long)dumy->lengthNT; i++)
|
||||
{
|
||||
extra_begin = extra_end = 0;
|
||||
currentID = dumy->overlapID[reverse_i--];
|
||||
x_start = MAX(window_start, (long long)overlap_list->list[currentID].x_pos_s);
|
||||
x_end = MIN(window_end, (long long)overlap_list->list[currentID].x_pos_e);
|
||||
|
||||
///overlap length between [window_start, window_end]
|
||||
x_len = x_end - x_start + 1;
|
||||
threshold = x_len * asm_opt.max_ov_diff_ec;
|
||||
/****************************may have bugs********************************/
|
||||
threshold = Adjust_Threshold(threshold, x_len);
|
||||
/****************************may have bugs********************************/
|
||||
|
||||
///offset of y
|
||||
y_start = (x_start - overlap_list->list[currentID].x_pos_s) + overlap_list->list[currentID].y_pos_s;
|
||||
/****************************may have bugs********************************/
|
||||
y_start += y_start_offset(x_start, &(overlap_list->list[currentID].f_cigar));
|
||||
/****************************may have bugs********************************/
|
||||
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
if(!determine_overlap_region(threshold, y_start, overlap_list->list[currentID].y_id, Window_Len, R_INF,
|
||||
&extra_begin, &extra_end, &y_start, &o_len))
|
||||
{
|
||||
append_window_list(&overlap_list->list[currentID], x_start, x_end,
|
||||
-1, -1, -1, -1, -1, -1);
|
||||
continue;
|
||||
}
|
||||
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand,
|
||||
R_INF, overlap_list->list[currentID].y_id, extra_begin, extra_end);
|
||||
|
||||
x_string = r_string + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
end_site = Reserve_Banded_BPM(y_string, Window_Len, x_string, x_len, threshold, &error);
|
||||
|
||||
if (error!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[currentID].align_length += x_len;
|
||||
append_window_list(&overlap_list->list[currentID], x_start, x_end, y_start, y_start + end_site, (int)error,
|
||||
extra_begin, extra_end, threshold);
|
||||
}
|
||||
else
|
||||
{
|
||||
append_window_list(&overlap_list->list[currentID], x_start, x_end, y_start, -1, -1,
|
||||
extra_begin, extra_end, threshold);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
inline double trim_error_rate(overlap_region_alloc* overlap_list, long long ID)
|
||||
{
|
||||
long long tLen, tError,i, subWinLen, subWinNum;
|
||||
@@ -7745,6 +7975,63 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
}
|
||||
|
||||
|
||||
void correct_ul_overlap(overlap_region_alloc* overlap_list, const ma_ug_t *uref,
|
||||
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
|
||||
Graph* g, Graph* DAGCon, Cigar_record* current_cigar,
|
||||
haplotype_evdience_alloc* hap, Round2_alignment* second_round,
|
||||
int force_repeat, int is_consensus, int* fully_cov, int* abnormal, double max_ov_diff_ec)
|
||||
{
|
||||
|
||||
clear_Correct_dumy(dumy, overlap_list);
|
||||
|
||||
long long window_start, window_end;
|
||||
|
||||
Window_Pool w_inf;
|
||||
|
||||
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/max_ov_diff_ec));
|
||||
|
||||
int flag = 0;
|
||||
|
||||
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)
|
||||
{
|
||||
dumy->length = 0;
|
||||
dumy->lengthNT = 0;
|
||||
flag = get_interval(window_start, window_end, overlap_list, dumy);
|
||||
|
||||
switch (flag)
|
||||
{
|
||||
case 1: ///no match here
|
||||
break;
|
||||
case 0: ///no match here
|
||||
break;
|
||||
case -2: ///if flag == -2, loop would be terminated
|
||||
break;
|
||||
}
|
||||
|
||||
|
||||
///dumy->lengthNT represent how many overlaps that the length of them is not equal to WINDOW; may larger or less than WINDOW
|
||||
///dumy->length represent how many overlaps that the length of them is WINDOW
|
||||
///now the windows which are larger than WINDOW are verified one-by-one, to improve it, we can do it group-bygroup
|
||||
verify_ul_window(window_start, window_end, overlap_list, dumy, uref, g_read->seq);
|
||||
}
|
||||
|
||||
/**
|
||||
// recalcate_window(overlap_list, R_INF, g_read, dumy, overlap_read);
|
||||
// partition_overlaps(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
|
||||
recalcate_window_advance(overlap_list, R_INF, g_read, dumy, overlap_read);
|
||||
partition_overlaps_advance(overlap_list, R_INF, g_read, overlap_read, dumy, hap, force_repeat);
|
||||
|
||||
if(is_consensus)
|
||||
{
|
||||
generate_consensus(overlap_list, R_INF, g_read, dumy, g, DAGCon, current_cigar, second_round);
|
||||
}
|
||||
|
||||
|
||||
(*fully_cov) = check_if_fully_covered(overlap_list, R_INF, g_read, dumy, g, abnormal);
|
||||
**/
|
||||
}
|
||||
|
||||
|
||||
void init_Cigar_record(Cigar_record* dummy)
|
||||
{
|
||||
dummy->length = 0;
|
||||
|
||||
Reference in New Issue
Block a user