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for break points at chr11

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This commit is contained in:
Haoyu Cheng
2019-12-12 00:31:24 -05:00
parent 09603432e5
commit f1cde019a9
5 changed files with 1426 additions and 186 deletions
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80
Assembly.cpp
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@@ -1919,8 +1919,9 @@ void* Overlap_calculate_heap_merge(void* arg)
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, THRESHOLD_RATE*1.5);
///get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.02);
clear_Cigar_record(&current_cigar);
clear_Round2_alignment(&second_round);
@@ -2119,8 +2120,8 @@ 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, THRESHOLD_RATE*1.5);
////get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.02);
fprintf(stderr, ">%.*s\n", Get_NAME_LENGTH((R_INF), i),
Get_NAME((R_INF), i));
@@ -2998,7 +2999,8 @@ void* Final_overlap_calculate_heap_merge(void* arg)
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
////get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.001);
/**
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,
@@ -3081,22 +3083,6 @@ 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;
@@ -3125,22 +3111,6 @@ 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, "\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++)
@@ -3171,23 +3141,6 @@ 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++;
@@ -3201,25 +3154,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
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");
// }
}