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r249: make max overlap error rate CLI options

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This commit is contained in:
Heng Li
2020-05-06 01:16:50 -04:00
parent 331e437c72
commit 3364a29b87
6 changed files with 56 additions and 49 deletions
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Correct.cpp
+18 -21
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@@ -260,7 +260,7 @@ All_reads* R_INF)
x_len = x_end - x_start + 1;
threshold = x_len * THRESHOLD_RATE;
threshold = x_len * asm_opt.max_ov_diff_ec;
/****************************may have bugs********************************/
threshold = Adjust_Threshold(threshold, x_len);
/****************************may have bugs********************************/
@@ -483,7 +483,7 @@ char* r_string)
///overlap length between [window_start, window_end]
x_len = x_end - x_start + 1;
threshold = x_len * THRESHOLD_RATE;
threshold = x_len * asm_opt.max_ov_diff_ec;
/****************************may have bugs********************************/
threshold = Adjust_Threshold(threshold, x_len);
/****************************may have bugs********************************/
@@ -548,8 +548,8 @@ inline double trim_error_rate(overlap_region_alloc* overlap_list, long long ID)
}
else
{
///tError += (Adjust_Threshold(subWinLen*THRESHOLD_RATE, subWinLen) * 2);
tError += (Adjust_Threshold(subWinLen*THRESHOLD_RATE, subWinLen) * 3);
///tError += (Adjust_Threshold(subWinLen*asm_opt.max_ov_diff_ec, subWinLen) * 2);
tError += Adjust_Threshold(subWinLen * asm_opt.max_ov_diff_ec, subWinLen) * 3;
}
}
}
@@ -566,8 +566,8 @@ inline double trim_error_rate(overlap_region_alloc* overlap_list, long long ID)
}
else
{
///tError += (Adjust_Threshold(subWinLen*THRESHOLD_RATE, subWinLen) * 2);
tError += (Adjust_Threshold(subWinLen*THRESHOLD_RATE, subWinLen) * 3);
///tError += (Adjust_Threshold(subWinLen*asm_opt.max_ov_diff_ec, subWinLen) * 2);
tError += Adjust_Threshold(subWinLen * asm_opt.max_ov_diff_ec, subWinLen) * 3;
}
}
}
@@ -2118,7 +2118,7 @@ inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_IN
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 = x_len * asm_opt.max_ov_diff_ec;
threshold = overlap_list->list[j].w_list[i].error_threshold;
/****************************may have bugs********************************/
/****************************may have bugs********************************/
@@ -2415,7 +2415,7 @@ UC_Read* g_read)
// }
threshold = xLen * THRESHOLD_RATE;
threshold = xLen * asm_opt.max_ov_diff_ec;
threshold = Adjust_Threshold(threshold, xLen);
threshold = double_error_threshold(threshold, xLen);
@@ -2931,7 +2931,7 @@ inline void recalcate_window_advance(overlap_region_alloc* overlap_list, All_rea
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 = x_len * asm_opt.max_ov_diff_ec;
threshold = overlap_list->list[j].w_list[i].error_threshold;
/****************************may have bugs********************************/
/****************************may have bugs********************************/
@@ -2998,19 +2998,16 @@ inline void recalcate_window_advance(overlap_region_alloc* overlap_list, All_rea
}
}
///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)
if(error_rate <= FINAL_OVERLAP_ERROR_RATE)
if (error_rate <= asm_opt.max_ov_diff_final)
{
overlap_list->mapped_overlaps_length += overlap_length;
overlap_list->list[j].is_match = 1;
calculate_boundary_cigars(&(overlap_list->list[j]), R_INF, dumy, g_read);
}
else if(error_rate <= 0.045)
else if (error_rate <= asm_opt.max_ov_diff_final * 1.5)
{
overlap_list->list[j].is_match = 3;
}
@@ -4552,7 +4549,7 @@ Cigar_record* current_cigar, long long uncorrected_window_start, Round2_alignmen
x_start = corrected_window_start;
x_end = corrected_window_end;
x_len = x_end - x_start + 1;
threshold = x_len * THRESHOLD_RATE;
threshold = x_len * asm_opt.max_ov_diff_ec;
/****************************may have bugs********************************/
threshold = Adjust_Threshold(threshold, x_len);
/****************************may have bugs********************************/
@@ -4741,7 +4738,7 @@ void generate_consensus(overlap_region_alloc* overlap_list, All_reads* R_INF,
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;
///for last window
@@ -4885,7 +4882,7 @@ All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy, Graph* g, int* abnormal)
(*abnormal) = 0;
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;
long long realLen = 0, tmpLen = 0;
@@ -6594,7 +6591,7 @@ Correct_dumy* dumy)
{
long long window_start, window_end;
Window_Pool w_inf;
init_Window_Pool(&w_inf, read_length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, read_length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;
long long realLen = 0, realLen_100 = 0;
int to_recover = 0;
@@ -7046,7 +7043,7 @@ void partition_overlaps(overlap_region_alloc* overlap_list, All_reads* R_INF,
long long num_availiable_win = 0;
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)
@@ -7135,7 +7132,7 @@ void partition_overlaps_advance(overlap_region_alloc* overlap_list, All_reads* R
long long num_availiable_win = 0;
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)
@@ -7219,7 +7216,7 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
int flag = 0;