xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-30 06:18:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

fix bugs for overlaps of different length

Browse Source
This commit is contained in:
Haoyu Cheng
2019-12-09 17:07:11 -05:00
parent fca9c8db15
commit 09603432e5
11 changed files with 1726 additions and 94 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Assembly.cpp
+272 -29
View File
@@ -29,6 +29,7 @@ int roundID = 0;
long long complete_threads = 0;
void* Perform_Counting(void* arg)
{
int thr_ID = *((int*)arg);
@@ -1237,7 +1238,7 @@ long long xBeg, long long xEnd, long long yBeg, long long yEnd)
}
long long push_final_overlaps(ma_hit_t_alloc* paf, ma_hit_t_alloc* reverse_paf_list,
overlap_region_alloc* overlap_list, UC_Read* x_read, UC_Read* y_read)
overlap_region_alloc* overlap_list, UC_Read* x_read, UC_Read* y_read, int flag, int test_exact)
{
long long i = 0;
long long available_overlaps = 0;
@@ -1245,7 +1246,8 @@ overlap_region_alloc* overlap_list, UC_Read* x_read, UC_Read* y_read)
clear_ma_hit_t_alloc(paf);
for (i = 0; i < overlap_list->length; i++)
{
if (overlap_list->list[i].is_match == 1)
///if (overlap_list->list[i].is_match == 1)
if (overlap_list->list[i].is_match == flag)
{
available_overlaps++;
/**********************query***************************/
@@ -1286,25 +1288,22 @@ overlap_region_alloc* overlap_list, UC_Read* x_read, UC_Read* y_read)
if(overlap_list->list[i].y_pos_strand == 0)
if(test_exact == 1)
{
recover_UC_Read(y_read, &R_INF, overlap_list->list[i].y_id);
if(overlap_list->list[i].y_pos_strand == 0)
{
recover_UC_Read(y_read, &R_INF, overlap_list->list[i].y_id);
}
else
{
recover_UC_Read_RC(y_read, &R_INF, overlap_list->list[i].y_id);
}
tmp.el = if_exact_match(x_read->seq, x_read->length, y_read->seq, y_read->length,
overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e,
overlap_list->list[i].y_pos_s, overlap_list->list[i].y_pos_e);
}
else
{
recover_UC_Read_RC(y_read, &R_INF, overlap_list->list[i].y_id);
}
tmp.el = if_exact_match(x_read->seq, x_read->length, y_read->seq, y_read->length,
overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e,
overlap_list->list[i].y_pos_s, overlap_list->list[i].y_pos_e);
add_ma_hit_t_alloc(paf, &tmp);
}
}
@@ -1911,16 +1910,23 @@ void* Overlap_calculate_heap_merge(void* arg)
init_small_hash_table(&reverse);
uint8_t c2n[256];
memset(c2n, 4, 256);
c2n['A'] = c2n['a'] = 0; c2n['C'] = c2n['c'] = 1;
c2n['G'] = c2n['g'] = 2; c2n['T'] = c2n['t'] = 3; // build the encoding table
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.02);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
clear_Cigar_record(&current_cigar);
clear_Round2_alignment(&second_round);
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
&current_cigar, &hap, &second_round, 0, 1, &fully_cov, &abnormal);
&current_cigar, &hap, &second_round, 0, 1, &fully_cov, &abnormal, c2n);
num_read_base = num_read_base + g_read.length;
num_correct_base = num_correct_base + correct.corrected_base;
@@ -2113,7 +2119,7 @@ void* Output_related_reads(void* arg)
&&
memcmp(required_read_name, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0)
{
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.02);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
fprintf(stderr, ">%.*s\n", Get_NAME_LENGTH((R_INF), i),
@@ -2815,6 +2821,77 @@ HeapSq* heap, Candidates_list* l)
}
void debug_print_overlap(char* y_name, overlap_region_alloc* overlap_list, All_reads* R_INF, char* func)
{
fprintf(stderr, "\nafter %s\n", func);
long long i, j;
for (i = 0; i < overlap_list->length; i++)
{
if(y_name == NULL || memcmp(y_name, Get_NAME((*R_INF), overlap_list->list[i].y_id),
Get_NAME_LENGTH((*R_INF), overlap_list->list[i].y_id)) == 0)
{
fprintf(stderr, "****************x_name: %.*s, x_id: %d****************\n",
Get_NAME_LENGTH((*R_INF), overlap_list->list[i].x_id),
Get_NAME((*R_INF), overlap_list->list[i].x_id), overlap_list->list[i].x_id);
fprintf(stderr, "y_name: %.*s, y_id: %d, is_match: %d\n",
Get_NAME_LENGTH((*R_INF),overlap_list->list[i].y_id),
Get_NAME((*R_INF),overlap_list->list[i].y_id), overlap_list->list[i].y_id,
overlap_list->list[i].is_match);
fprintf(stderr, "alignLen: %d, x_s: %d, x_e: %d, y_s: %d, y_e: %d, y_dir: %d, strong: %d\n",
overlap_list->list[i].align_length,
overlap_list->list[i].x_pos_s,
overlap_list->list[i].x_pos_e,
overlap_list->list[i].y_pos_s,
overlap_list->list[i].y_pos_e,
overlap_list->list[i].y_pos_strand,
overlap_list->list[i].strong);
fprintf(stderr, "i: %d, %.*s, x_s: %d, x_e: %d, y_s: %d, y_end: %d, w_list_length: %d, dir: %d, strong: %d, is_match: %d\n",
i, Get_NAME_LENGTH((*R_INF),overlap_list->list[i].y_id),
Get_NAME((*R_INF),overlap_list->list[i].y_id),
overlap_list->list[i].x_pos_s,
overlap_list->list[i].x_pos_e,
overlap_list->list[i].y_pos_s,
overlap_list->list[i].y_pos_e,
overlap_list->list[i].w_list_length,
overlap_list->list[i].y_pos_strand,
overlap_list->list[i].strong,
overlap_list->list[i].is_match);
for (j = 0; j < overlap_list->list[i].w_list_length; j++)
{
fprintf(stderr, "************************\ncigar_j: %d, x_s: %d, x_e: %d, y_s: %d, y_end: %d\n",
j, overlap_list->list[i].w_list[j].x_start,
overlap_list->list[i].w_list[j].x_end,
overlap_list->list[i].w_list[j].y_start,
overlap_list->list[i].w_list[j].y_end);
if(overlap_list->list[i].w_list[j].y_end == -1)
{
fprintf(stderr, "not match\n");
}
else
{
int cigar_i, operation, operationLen;
CIGAR* cigar = &(overlap_list->list[i].w_list[j].cigar);
fprintf(stderr, "length: %d\n", cigar->length);
for (cigar_i = 0; cigar_i < cigar->length; cigar_i++)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
fprintf(stderr, "oper: %d, Len: %d\n", operation, operationLen);
}
}
}
}
}
}
void* Final_overlap_calculate_heap_merge(void* arg)
{
long long matched_overlap_0 = 0;
@@ -2892,10 +2969,36 @@ void* Final_overlap_calculate_heap_merge(void* arg)
init_small_hash_table(&reverse);
long long pre_r_overlaps = 0;
long long cur_r_overlaps = 0;
long long pre_overlaps = 0;
long long cur_overlaps = 0;
if(thr_ID == 0)
{
for (i = 0; i < R_INF.total_reads; i++)
{
pre_r_overlaps += R_INF.reverse_paf[i].length;
pre_overlaps += R_INF.paf[i].length;
}
}
// if(thr_ID == 0)
// {
// debug_info_of_specfic_read("m64016_190918_162737/130811282/ccs",
// R_INF.paf, R_INF.reverse_paf, -1, "xxxx");
// debug_info_of_specfic_read("m64016_190918_162737/179635219/ccs",
// R_INF.paf, R_INF.reverse_paf, -1, "xxxx");
// }
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
///0.1%
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.001);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
/**
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
@@ -2906,9 +3009,25 @@ void* Final_overlap_calculate_heap_merge(void* arg)
overlap_region_sort_y_id(overlap_list.list, overlap_list.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);
ma_hit_sort_tn(R_INF.reverse_paf[i].buffer, R_INF.reverse_paf[i].length);
// if(memcmp("m64016_190918_162737/130811282/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n1\n");
// debug_print_overlap("m64016_190918_162737/179635219/ccs", &overlap_list, &R_INF, "first");
// }
// if(memcmp("m64016_190918_162737/179635219/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n1\n");
// debug_print_overlap("m64016_190918_162737/130811282/ccs", &overlap_list, &R_INF, "first");
// }
overlap_list.mapped_overlaps_length = 0;
inner_j = 0;
@@ -2961,6 +3080,67 @@ void* Final_overlap_calculate_heap_merge(void* arg)
}
// if(memcmp("m64016_190918_162737/130811282/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n2\n");
// debug_print_overlap("m64016_190918_162737/179635219/ccs", &overlap_list, &R_INF, "second");
// }
// if(memcmp("m64016_190918_162737/179635219/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n2\n");
// debug_print_overlap("m64016_190918_162737/130811282/ccs", &overlap_list, &R_INF, "second");
// }
inner_j = 0;
j = 0;
while (j < overlap_list.length && inner_j < R_INF.reverse_paf[i].length)
{
if(overlap_list.list[j].y_id < R_INF.reverse_paf[i].buffer[inner_j].tn)
{
j++;
}
else if(overlap_list.list[j].y_id > R_INF.reverse_paf[i].buffer[inner_j].tn)
{
inner_j++;
}
else
{
if(overlap_list.list[j].y_pos_strand == R_INF.reverse_paf[i].buffer[inner_j].rev)
{
overlap_list.list[j].is_match = 2;
overlap_list.list[j].strong = 0;
overlap_list.list[j].without_large_indel = 1;
}
j++;
inner_j++;
}
}
// if(memcmp("m64016_190918_162737/130811282/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n3\n");
// debug_print_overlap("m64016_190918_162737/179635219/ccs", &overlap_list, &R_INF, "third");
// }
// if(memcmp("m64016_190918_162737/179635219/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n3\n");
// debug_print_overlap("m64016_190918_162737/130811282/ccs", &overlap_list, &R_INF, "third");
// }
///recover missing exact overlaps
reverse_complement(g_read.seq, g_read.length);
for (j = 0; j < overlap_list.length; j++)
@@ -2991,18 +3171,60 @@ void* Final_overlap_calculate_heap_merge(void* arg)
}
// if(memcmp("m64016_190918_162737/130811282/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n4\n");
// debug_print_overlap("m64016_190918_162737/179635219/ccs", &overlap_list, &R_INF, "fourth");
// }
// if(memcmp("m64016_190918_162737/179635219/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n4\n");
// debug_print_overlap("m64016_190918_162737/130811282/ccs", &overlap_list, &R_INF, "fourth");
// }
if(R_INF.paf[i].is_fully_corrected)
{
potiental_matched_overlap_1++;
}
num_correct_base +=
push_final_overlaps(&(R_INF.paf[i]), R_INF.reverse_paf, &overlap_list, &g_read, &overlap_read);
push_final_overlaps(&(R_INF.paf[i]), R_INF.reverse_paf,
&overlap_list, &g_read, &overlap_read, 1, 1);
push_final_overlaps(&(R_INF.reverse_paf[i]), R_INF.reverse_paf,
&overlap_list, &g_read, &overlap_read, 2, 0);
// if(memcmp("m64016_190918_162737/130811282/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n5\n");
// debug_print_overlap("m64016_190918_162737/179635219/ccs", &overlap_list, &R_INF, "last");
// debug_print_overlap(NULL, &overlap_list, &R_INF, "SET");
// }
// if(memcmp("m64016_190918_162737/179635219/ccs", Get_NAME((R_INF), i),
// Get_NAME_LENGTH((R_INF), i)) == 0)
// {
// fprintf(stderr, "\n5\n");
// debug_print_overlap("m64016_190918_162737/130811282/ccs", &overlap_list, &R_INF, "last");
// debug_print_overlap(NULL, &overlap_list, &R_INF, "SET");
// }
}
finish_output_buffer();
destory_buffer_sub_block(&current_sub_buffer);
@@ -3045,11 +3267,32 @@ void* Final_overlap_calculate_heap_merge(void* arg)
fprintf(stderr, "fully corrected reads: %llu\n", total_potiental_matched_overlap_1);
for (i = 0; i < R_INF.total_reads; i++)
{
cur_r_overlaps += R_INF.reverse_paf[i].length;
cur_overlaps += R_INF.paf[i].length;
}
fprintf(stderr, "pre_r_overlaps: %d, cur_r_overlaps: %d\n",
pre_r_overlaps, cur_r_overlaps);
fprintf(stderr, "pre_overlaps: %d, cur_overlaps: %d\n",
pre_overlaps, cur_overlaps);
// debug_info_of_specfic_read("m64016_190918_162737/130811282/ccs",
// R_INF.paf, R_INF.reverse_paf, -1, "yyyy");
// debug_info_of_specfic_read("m64016_190918_162737/179635219/ccs",
// R_INF.paf, R_INF.reverse_paf, -1, "yyyy");
}
pthread_mutex_unlock(&statistics);
free(arg);
}
@@ -3134,7 +3377,7 @@ void generate_overlaps(int last_round)
fprintf(stdout, "Final overlaps have been calculated.\n");
fprintf(stdout, "%-30s%18.2f\n\n", "Final overlaps calculation time:", Get_T() - start_time);
///Output_PAF();
Output_PAF();
/**
build_string_graph(MIN_OVERLAP_COVERAGE, R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, R_INF.read_length,
MIN_OVERLAP_LEN, MAX_HANG_LEN, 3, 0.5, 0.7, 0.8, output_file_name, MAX_BUBBLE_DIST);