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This commit is contained in:
Haoyu Cheng
2019-12-28 04:45:53 -05:00
parent 8f549c1c16
commit 1523d10291
11 changed files with 831 additions and 107 deletions
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Assembly.cpp
+21 -19
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@@ -297,7 +297,7 @@ void Counting_multiple_thr()
if (asm_opt.roundID == 0)
{
init_kseq(asm_opt.read_file_name);
init_gz_files(&asm_opt);
init_All_reads(&R_INF);
init_R_buffer(asm_opt.thread_num);
pthread_create(&inputReadsHandle, NULL, input_reads_muti_threads, (void*)is_insert);
@@ -336,7 +336,8 @@ void Counting_multiple_thr()
if (asm_opt.roundID == 0)
{
pthread_join(inputReadsHandle, NULL);
destory_kseq();
///destory_kseq();
destory_gz_files();
}
fprintf(stderr, "Counting has been completed.\n");
@@ -372,12 +373,9 @@ void Build_hash_table_multiple_thr()
if (asm_opt.roundID == 0)
{
init_kseq(asm_opt.read_file_name);
init_gz_files(&asm_opt);
clear_R_buffer();
malloc_All_reads(&R_INF);
pthread_create(&inputReadsHandle, NULL, input_reads_muti_threads, (void*)is_insert);
}
@@ -422,7 +420,8 @@ void Build_hash_table_multiple_thr()
if (asm_opt.roundID == 0)
{
destory_kseq();
///destory_kseq();
destory_gz_files();
destory_R_buffer();
}
@@ -1234,7 +1233,10 @@ void Output_corrected_reads()
long long i;
UC_Read g_read;
init_UC_Read(&g_read);
FILE* output_file = fopen(asm_opt.output_file_name, "w");
char* gfa_name = (char*)malloc(strlen(asm_opt.output_file_name)+35);
sprintf(gfa_name, "%s.ec.fa", asm_opt.output_file_name);
FILE* output_file = fopen(gfa_name, "w");
free(gfa_name);
for (i = 0; i < (long long)R_INF.total_reads; i++)
{
@@ -1325,18 +1327,18 @@ 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;
}
// 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,