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for hifiasm 3.0

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chhylp123
2020-03-22 16:54:32 -04:00
parent 6ae51c84f6
commit c72d419711
16 changed files with 38378 additions and 654 deletions
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Assembly.cpp
+7 -22
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@@ -9,6 +9,7 @@
#include "POA.h"
#include "Correct.h"
#include "Output.h"
#include "Trio.h"
Total_Count_Table TCB;
Total_Pos_Table PCB;
@@ -1257,7 +1258,7 @@ void Overlap_calculate_multipe_thr()
double start_time = Get_T();
fprintf(stderr, "Begin calculating overlaps... \n");
pthread_t *_r_threads;
_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*asm_opt.thread_num);
@@ -1327,19 +1328,6 @@ void Overlap_calculate_multipe_thr()
}
// int load_pre_cauculated_index()
// {
// if(load_Total_Pos_Table(&PCB, asm_opt.read_file_name) && load_All_reads(&R_INF, asm_opt.read_file_name))
// {
// return 1;
// }
// else
// {
// return 0;
// }
// }
void update_overlaps(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf,
UC_Read* g_read, UC_Read* overlap_read, int is_match, int is_exact)
@@ -1758,7 +1746,7 @@ void Output_PAF()
free(paf_name);
fclose(output_file);
fprintf(stderr, "PAF has beem written.\n");
fprintf(stderr, "PAF has been written.\n");
}
@@ -1838,9 +1826,6 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
if((long long)edge_vector.n >= rescue_threshold &&
check_cluster(edge_vector.a, edge_vector.n, paf, cluster_threshold) == 1)
{
// fprintf(stderr,"\nremove following %u edges...\n", edge_vector.n);
// print_revise_edges(&(paf[i]), edge_vector_index.a, edge_vector_index.n);
add_overlaps(&(paf[i]), &(rev_paf[i]), edge_vector_index.a, edge_vector_index.n);
remove_overlaps(&(paf[i]), edge_vector_index.a, edge_vector_index.n);
revises = revises + edge_vector.n;
@@ -1868,10 +1853,6 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
if((long long)edge_vector.n >= rescue_threshold &&
check_cluster(edge_vector.a, edge_vector.n, paf, cluster_threshold) == 1)
{
// fprintf(stderr,"\nadd following %u edges...\n", edge_vector.n);
// print_revise_edges(&(rev_paf[i]), edge_vector_index.a, edge_vector_index.n);
remove_overlaps(&(rev_paf[i]), edge_vector_index.a, edge_vector_index.n);
add_overlaps_from_different_sources(paf, &(paf[i]), edge_vector.a, edge_vector.n);
revises = revises + edge_vector.n;
@@ -1886,6 +1867,7 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
}
void generate_overlaps(int last_round)
{
double start_time = Get_T();
@@ -1914,11 +1896,14 @@ void generate_overlaps(int last_round)
free(_r_threads);
///rescue_edges(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, 4, 0.985);
destory_Total_Pos_Table(&PCB);
fprintf(stderr, "Final overlaps have been calculated.\n");
fprintf(stderr, "%-30s%18.2f\n\n", "Final overlaps calculation time:", Get_T() - start_time);
Output_PAF();
trio_partition();
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,