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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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CommandLines.cpp
+21 -6
View File
@@ -10,11 +10,13 @@
hifiasm_opt_t asm_opt;
static ko_longopt_t long_options[] = {
{ "version", ko_no_argument, 300 },
{ "dbg-gfa", ko_no_argument, 301 },
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "version", ko_no_argument, 300 },
{ "dbg-gfa", ko_no_argument, 301 },
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "max-od-ec", ko_no_argument, 305 },
{ "max-od-final", ko_no_argument, 306 },
{ 0, 0, 0 }
};
@@ -83,7 +85,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->k_mer_length = 51;
asm_opt->mz_win = 51;
asm_opt->bf_shift = 37;
asm_opt->high_factor = 5.0f;
asm_opt->high_factor = 5.0;
asm_opt->max_ov_diff_ec = 0.04;
asm_opt->max_ov_diff_final = 0.03;
asm_opt->hom_cov = 20;
asm_opt->max_n_chain = 100;
asm_opt->k_mer_min_freq = 3;
@@ -264,6 +268,15 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if (asm_opt->max_ov_diff_ec < asm_opt->max_ov_diff_final) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than max_ov_diff_final\n");
return 0;
}
if (asm_opt->max_ov_diff_ec < HA_MIN_OV_DIFF) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than %g\n", HA_MIN_OV_DIFF);
return 0;
}
if(asm_opt->max_short_tip < 0)
{
@@ -385,6 +398,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;
else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
else if (c == 305) asm_opt->max_ov_diff_ec = atof(opt.arg);
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
CommandLines.h
+13 -9
View File
@@ -3,18 +3,20 @@
#include <pthread.h>
#define HA_VERSION "0.5-dirty-r248"
#define HA_VERSION "0.5-dirty-r249"
#define VERBOSE 0
#define HA_F_NO_HPC 0x1
#define HA_F_NO_KMER_FLT 0x2
#define HA_F_VERBOSE_GFA 0x4
#define HA_F_WRITE_EC 0x8
#define HA_F_WRITE_PAF 0x10
#define HA_F_SKIP_TRIOBIN 0x20
#define HA_F_NO_HPC 0x1
#define HA_F_NO_KMER_FLT 0x2
#define HA_F_VERBOSE_GFA 0x4
#define HA_F_WRITE_EC 0x8
#define HA_F_WRITE_PAF 0x10
#define HA_F_SKIP_TRIOBIN 0x20
#define HA_F_PURGE_CONTAIN 0x40
#define HA_F_PURGE_JOIN 0x80
#define HA_F_PURGE_JOIN 0x80
#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
typedef struct {
int flag;
@@ -28,7 +30,9 @@ typedef struct {
int k_mer_length;
int mz_win;
int bf_shift;
float high_factor; // coverage cutoff set to high_factor*hom_cov
double high_factor; // coverage cutoff set to high_factor*hom_cov
double max_ov_diff_ec;
double max_ov_diff_final;
int hom_cov;
int max_n_chain; // fall-back max number of chains to consider
int k_mer_min_freq;
Correct.cpp
+18 -21
View File
@@ -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;
Correct.h
+1
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@@ -16,6 +16,7 @@
#define INSERTION 2
#define DELETION 3
#define WINDOW_MAX_SIZE (WINDOW + (int)(1.0 / HA_MIN_OV_DIFF) + 3) // TODO: why 1/max_ov_diff?
///#define FLAG_THRE 0
Hash_Table.h
-9
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@@ -6,22 +6,13 @@
#define MAX_SUFFIX_BITS 64
#define MODE_VALUE 101
///#define WINDOW 350
///#define THRESHOLD 14
#define WINDOW 375
//#define WINDOW_BOUNDARY 150
#define WINDOW_BOUNDARY 375
///for one side, the first or last WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY bases should not be corrected
#define WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY 25
#define THRESHOLD 15
#define THRESHOLD_RATE 0.04
#define TAIL_LENGTH int(1/THRESHOLD_RATE)
///#define OVERLAP_THRESHOLD 0.9
#define OVERLAP_THRESHOLD_FILTER 0.9
#define WINDOW_MAX_SIZE WINDOW + TAIL_LENGTH + 3
#define THRESHOLD_MAX_SIZE 31
#define FINAL_OVERLAP_ERROR_RATE 0.03
#define GROUP_SIZE 4
///the max cigar likes 10M10D10M10D10M
Overlaps.cpp
+3 -4
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@@ -1725,10 +1725,9 @@ ma_sub_t* coverage_cut, float shift_rate)
collect_contain(&(paf[i]), NULL, rLen, &max_left, &max_right, 0.1);
///collect_contain(&(paf[i]), &(rev_paf[i]), rLen, &max_left, &max_right, 0.1);
////shift_rate should be (FINAL_OVERLAP_ERROR_RATE*2)
////shift_rate should be (asm_opt.max_ov_diff_final*2)
///this read is a normal read
if(max_left.e > max_right.s &&
(max_left.e - max_right.s >= rLen * shift_rate))
if (max_left.e > max_right.s && (max_left.e - max_right.s >= rLen * shift_rate))
{
continue;
}
@@ -26062,7 +26061,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///ma_hit_sub is just use to init coverage_cut,
///it seems we do not need ma_hit_cut & ma_hit_flt
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, FINAL_OVERLAP_ERROR_RATE*2);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, asm_opt.max_ov_diff_final * 2.0);
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///print_binned_reads(sources, n_read, coverage_cut);
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);