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NOT WORKING!!! backup only

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This commit is contained in:
Heng Li
2020-03-24 00:44:56 -04:00
parent e6ef2fb56f
commit 59a9d62df9
8 changed files with 131 additions and 714 deletions
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Assembly.cpp
+6 -72
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@@ -225,7 +225,6 @@ void* Build_hash_table(void* arg)
int avalible_k = 0;
while (file_flag != 0)
{
@@ -802,13 +801,11 @@ overlap_region_alloc* overlap_list, int flag)
}
}
return available_overlaps;
}
void get_new_candidates(long long readID, UC_Read* g_read, overlap_region_alloc* overlap_list, k_mer_pos_list_alloc* array_list,
HeapSq* heap, Candidates_list* l, double band_width_threshold, int keep_whole_chain)
Candidates_list* l, double band_width_threshold, int keep_whole_chain)
{
HPC_seq HPC_read;
Hash_code k_code;
@@ -819,7 +816,6 @@ HeapSq* heap, Candidates_list* l, double band_width_threshold, int keep_whole_ch
uint64_t list_length;
uint64_t sub_ID;
clear_Heap(heap);
clear_Candidates_list(l);
clear_k_mer_pos_list_alloc(array_list);
@@ -827,18 +823,15 @@ HeapSq* heap, Candidates_list* l, double band_width_threshold, int keep_whole_ch
recover_UC_Read(g_read, &R_INF, readID);
///forward strand
init_HPC_seq(&HPC_read, g_read->seq, g_read->length);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code, asm_opt.k_mer_length);
k_mer_append(&k_code, code, asm_opt.k_mer_length);
avalible_k++;
if (avalible_k >= asm_opt.k_mer_length)
{
@@ -857,38 +850,8 @@ HeapSq* heap, Candidates_list* l, double band_width_threshold, int keep_whole_ch
}
}
// BIG CHANGES WILL GO HERE!!!
///reverse complement strand
reverse_complement(g_read->seq, g_read->length);
init_HPC_seq(&HPC_read, g_read->seq, g_read->length);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code, asm_opt.k_mer_length);
avalible_k++;
if (avalible_k >= asm_opt.k_mer_length)
{
list_length = locate_Total_Pos_Table(&PCB, &k_code, &list, asm_opt.k_mer_length, &sub_ID);
if (list_length != 0)
{
append_k_mer_pos_list_alloc(array_list, list, list_length, end_pos, 1);
}
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
}
merge_k_mer_pos_list_alloc_heap_sort(array_list, l, heap);
calculate_overlap_region_by_chaining(l, overlap_list, readID, g_read->length, &R_INF,
band_width_threshold, keep_whole_chain);
}
@@ -922,10 +885,6 @@ void* Overlap_calculate_heap_merge(void* arg)
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
HeapSq heap;
Init_Heap(&heap);
Correct_dumy correct;
init_Correct_dumy(&correct);
@@ -946,7 +905,7 @@ void* Overlap_calculate_heap_merge(void* arg)
for (i = thr_ID; i < (long long)R_INF.total_reads; i = i + asm_opt.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, 0.02, 1);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.02, 1);
clear_Cigar_record(&current_cigar);
clear_Round2_alignment(&second_round);
@@ -982,7 +941,6 @@ void* Overlap_calculate_heap_merge(void* arg)
destory_buffer_sub_block(&current_sub_buffer);
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_Heap(&heap);
destory_k_mer_pos_list_alloc(&array_list);
destory_Graph(&POA_Graph);
destory_Graph(&DAGCon);
@@ -1040,9 +998,6 @@ void* Output_related_reads(void* arg)
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
HeapSq heap;
Init_Heap(&heap);
Correct_dumy correct;
init_Correct_dumy(&correct);
@@ -1072,7 +1027,7 @@ void* Output_related_reads(void* arg)
memcmp(asm_opt.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, 0.02, 1);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.02, 1);
fprintf(stderr, ">%.*s\n", (int)Get_NAME_LENGTH((R_INF), i),
Get_NAME((R_INF), i));
@@ -1097,7 +1052,6 @@ void* Output_related_reads(void* arg)
destory_buffer_sub_block(&current_sub_buffer);
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_Heap(&heap);
destory_k_mer_pos_list_alloc(&array_list);
destory_Graph(&POA_Graph);
destory_Graph(&DAGCon);
@@ -1626,9 +1580,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
HeapSq heap;
Init_Heap(&heap);
Cigar_record_alloc cigarline;
init_Cigar_record_alloc(&cigarline);
@@ -1636,15 +1587,11 @@ void* Final_overlap_calculate_heap_merge(void* arg)
memset(c2n, 4, 256);
c2n[(uint8_t)'A'] = c2n[(uint8_t)'a'] = 0; c2n[(uint8_t)'C'] = c2n[(uint8_t)'c'] = 1;
c2n[(uint8_t)'G'] = c2n[(uint8_t)'g'] = 2; c2n[(uint8_t)'T'] = c2n[(uint8_t)'t'] = 3; // build the encoding table
for (i = thr_ID; i < R_INF.total_reads; i = i + asm_opt.thread_num)
{
get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, 0.001, 0);
get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
/**
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,
@@ -1677,7 +1624,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_Heap(&heap);
destory_k_mer_pos_list_alloc(&array_list);
destory_UC_Read(&g_read);
destory_UC_Read(&overlap_read);
@@ -1946,15 +1892,3 @@ void Correct_Reads(int last_round)
Correct_Reads(last_round - 1);
}