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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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Correct.h
+13 -309
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@@ -16,12 +16,11 @@
#define INSERTION 2
#define DELETION 3
#define MIN(x,y) ((x)<=(y)?(x):(y))
///#define FLAG_THRE 0
#define MAX(x, y) ((x >= y)?x:y)
#define MIN(x, y) ((x <= y)?x:y)
#define MAX(x, y) ((x >= y)?(x):(y))
#define MIN(x, y) ((x <= y)?(x):(y))
#define DIFF(x, y) ((MAX((x), (y))) - (MIN((x), (y))))
#define OVERLAP(x_start, x_end, y_start, y_end) (MIN(x_end, y_end) - MAX(x_start, y_start) + 1)
///#define OVERLAP(x_start, x_end, y_start, y_end) MIN(x_end, y_end) - MAX(x_start, y_start) + 1
@@ -37,8 +36,6 @@
#define Adjust_Threshold(threshold, x_len) ((threshold == 0 && x_len >= 4)? 1: threshold)
typedef struct
{
long long read_length;
@@ -67,7 +64,6 @@ inline void init_Window_Pool(Window_Pool* dumy, long long read_length, long long
dumy->window_num = (dumy->read_length + dumy->window_length - 1) / dumy->window_length;
}
inline int get_Window(Window_Pool* dumy, long long* w_beg, long long* w_end)
{
(*w_beg) = dumy->window_start;
@@ -92,28 +88,10 @@ inline int get_Window(Window_Pool* dumy, long long* w_beg, long long* w_end)
{
dumy->window_end = dumy->read_length - 1;
}
// else if (dumy->read_length - dumy->window_end - 1 <= dumy->tail_length)
// {
// dumy->window_end = dumy->read_length - 1;
// }
/**
if((*w_end) - (*w_beg) + 1 < 375 && (*w_end) + 1 != dumy->read_length)
{
fprintf(stderr, "(*w_beg):%d, (*w_end): %d, dumy->read_length: %d\n",
(*w_beg), (*w_end), dumy->read_length);
}
**/
return 1;
}
typedef struct
{
/**[0-1] bits are type:**/
@@ -326,45 +304,6 @@ inline int filter_one_snp(int occ_0, int occ_1, int total)
return 1;
}
inline int filter_one_snp_advance_back(int occ_0, int occ_1, int total, int group_size,
long long homopolymer_num, long long non_homopolymer_num)
{
double available;
if(occ_0 <= occ_1)
{
available = occ_0;
}
else
{
available = occ_1;
}
int min = available;
double threshold1 = 0.35;
double threshold2 = 0.24;
available = available/((double)(total));
//if(non_homopolymer_num > 0 && min >= 5 && group_size > 1)
if(non_homopolymer_num > 0 && min >= 5)
{
if(available < threshold2 || total < 10)
{
return 0;
}
}
else if(available < threshold1 || occ_0 < MIN_COVERAGE_THRESHOLD + 1 || total < 10)
{
return 0;
}
return 1;
}
inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int SNPsLen, int* nearsnp, int* non_nearsnps)
{
long long i, current_id, large_id, small_id;
@@ -502,96 +441,6 @@ uint32_t* SNPs, int SNPsLen)
return 1;
}
/**
inline int if_is_homopolymer(long long site, char* read, long long read_length)
{
long long beg, end, i;
beg = site - 10;
if(beg < 0)
{
beg = 0;
}
end = site + 10;
if(end >= read_length)
{
end = read_length - 1;
}
char f_homopolymer_ch = 0;
long long f_homopolymer_len = 0;
for (i = site + 1; i <= end; i++)
{
if(f_homopolymer_ch == 0)
{
f_homopolymer_ch = read[i];
f_homopolymer_len = 1;
}
else
{
if(read[i] != f_homopolymer_ch)
{
break;
}
else
{
f_homopolymer_len++;
}
}
}
char b_homopolymer_ch = 0;
long long b_homopolymer_len = 0;
for (i = site - 1; i >= beg; i--)
{
if(b_homopolymer_ch == 0)
{
b_homopolymer_ch = read[i];
b_homopolymer_len = 1;
}
else
{
if(read[i] != b_homopolymer_ch)
{
break;
}
else
{
b_homopolymer_len++;
}
}
}
if(f_homopolymer_ch == read[site])
{
f_homopolymer_len++;
}
else if(b_homopolymer_ch == read[site])
{
b_homopolymer_len++;
}
if(f_homopolymer_len >= 5 || b_homopolymer_len >= 5)
{
return 1;
}
if (b_homopolymer_ch == f_homopolymer_ch
&&
(f_homopolymer_len + b_homopolymer_len >= 5))
{
return 1;
}
return 0;
}
**/
inline int if_is_homopolymer_strict(long long site, char* read, long long read_length)
{
@@ -666,22 +515,6 @@ inline int if_is_homopolymer_strict(long long site, char* read, long long read_l
b_homopolymer_len++;
}
/**
fprintf(stderr, "site: %d, beg: %d, end: %d\n", site, beg, end);
for (i = beg; i <= end; i++)
{
if (i == site)
{
fprintf(stderr, "|%c|", read[i]);
}
else
{
fprintf(stderr, "%c", read[i]);
}
}
fprintf(stderr, "\n");
**/
if(f_homopolymer_len >= threshold || b_homopolymer_len >= threshold)
{
return 1;
@@ -774,22 +607,6 @@ inline int if_is_homopolymer_repeat(long long site, char* read, long long read_l
b_homopolymer_len++;
}
/**
fprintf(stderr, "site: %d, beg: %d, end: %d\n", site, beg, end);
for (i = beg; i <= end; i++)
{
if (i == site)
{
fprintf(stderr, "|%c|", read[i]);
}
else
{
fprintf(stderr, "%c", read[i]);
}
}
fprintf(stderr, "\n");
**/
if(f_homopolymer_len >= threshold || b_homopolymer_len >= threshold)
{
return 1;
@@ -825,8 +642,6 @@ UC_Read* g_read)
h->snp_stat[h->available_snp].is_homopolymer =
if_is_homopolymer_strict(h->snp_stat[h->available_snp].site, g_read->seq, g_read->length);
///fprintf(stderr, "is_homopolymer: %d\n", h->snp_stat[h->available_snp].is_homopolymer);
int8_t* vector = Get_SNP_Vector((*h), h->available_snp);
for (i = 0; i < sub_length; i++)
{
@@ -1053,7 +868,7 @@ inline void insert_SNP_IDs_addition(Snp_ID_Vector_Alloc* SNP_IDs, uint32_t* IDs_
}
inline void init_DP_matrix(DP_matrix* dp, int32_t snp_num)
inline void init_DP_matrix(DP_matrix* dp, uint32_t snp_num)
{
if(snp_num > dp->snp_size)
@@ -1147,9 +962,6 @@ inline void destoryHaplotypeEvdience(haplotype_evdience_alloc* h)
free(h->dp.buffer);
free(h->dp.max_buffer);
destory_SNP_IDs(&(h->dp.SNP_IDs));
}
inline void ResizeInitHaplotypeEvdience(haplotype_evdience_alloc* h)
@@ -1237,115 +1049,22 @@ void clear_Round2_alignment(Round2_alignment* h);
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read, Graph* g, Graph* DAGCon,
long long* matched_overlap_0, long long* matched_overlap_1,
long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1,
Cigar_record* current_cigar, haplotype_evdience_alloc* hap,
Round2_alignment* second_round, int force_repeat, int is_consensus,
int* fully_cov, int* abnormal, uint8_t* c2n);
int* fully_cov, int* abnormal);
void init_Correct_dumy(Correct_dumy* list);
void destory_Correct_dumy(Correct_dumy* list);
void clear_Correct_dumy(Correct_dumy* list, overlap_region_alloc* overlap_list);
void clear_Correct_dumy_pure(Correct_dumy* list);
void pre_filter_by_nearby(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read,
All_reads* R_INF, Correct_dumy* dumy, uint64_t* new_n_length);
void pre_filter_by_nearby_single(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read,
All_reads* R_INF, Correct_dumy* dumy, uint64_t* new_n_length);
void get_seq_from_Graph(Graph* backbone, Graph* DAGCon, Correct_dumy* dumy, Cigar_record* current_cigar, char* self_string,
char* r_string, long long r_string_length, long long r_string_site);
void init_Cigar_record(Cigar_record* dummy);
void destory_Cigar_record(Cigar_record* dummy);
void clear_Cigar_record(Cigar_record* dummy);
inline void add_new_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type)
{
uint32_t tmp;
tmp = len;
tmp = tmp << 2;
tmp = tmp | type;
dummy->length++;
if(dummy->length > dummy->size)
{
dummy->size = dummy->size * 2;
dummy->record = (uint32_t*)realloc(dummy->record, dummy->size*sizeof(uint32_t));
}
dummy->record[dummy->length - 1] = tmp;
}
inline void add_existing_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type)
{
uint32_t tmp;
tmp = dummy->record[dummy->length - 1] >> 2;
tmp = tmp + len;
tmp = tmp << 2;
tmp = tmp | type;
dummy->record[dummy->length - 1] = tmp;
}
inline void add_new_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint32_t len, uint32_t type, char* seq)
{
uint32_t tmp;
tmp = len;
tmp = tmp << 2;
tmp = tmp | type;
dummy->length++;
if(dummy->length > dummy->size)
{
dummy->size = dummy->size * 2;
dummy->record = (uint32_t*)realloc(dummy->record, dummy->size*sizeof(uint32_t));
}
dummy->record[dummy->length - 1] = tmp;
if (dummy->lost_base_length + len> dummy->lost_base_size)
{
dummy->lost_base_size = (dummy->lost_base_length + len) * 2;
dummy->lost_base = (char*)realloc(dummy->lost_base, dummy->lost_base_size*sizeof(char));
}
int i = 0;
for (i = 0; i < len; i++, dummy->lost_base_length++)
{
dummy->lost_base[dummy->lost_base_length] = seq[i];
}
}
inline void add_existing_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint32_t len, uint32_t type, char* seq)
{
uint32_t tmp;
tmp = dummy->record[dummy->length - 1] >> 2;
tmp = tmp + len;
tmp = tmp << 2;
tmp = tmp | type;
dummy->record[dummy->length - 1] = tmp;
if (dummy->lost_base_length + len> dummy->lost_base_size)
{
dummy->lost_base_size = (dummy->lost_base_length + len) * 2;
dummy->lost_base = (char*)realloc(dummy->lost_base, dummy->lost_base_size*sizeof(char));
}
int i = 0;
for (i = 0; i < len; i++, dummy->lost_base_length++)
{
dummy->lost_base[dummy->lost_base_length] = seq[i];
}
}
void add_new_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type);
void add_existing_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type);
void add_new_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint32_t len, uint32_t type, char* seq);
void add_existing_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint32_t len, uint32_t type, char* seq);
/***
@@ -1356,15 +1075,11 @@ inline void add_existing_cell_to_cigar_record_with_different_base(Cigar_record*
3. deletion
***/
inline void add_cigar_record(char* seq, uint32_t len, Cigar_record* dummy, uint32_t type)
{
uint32_t tmp;
{
if(type == 0)///match
{
///add to existing cell, just increase length
if(dummy->current_operation == type)
if((uint32_t)dummy->current_operation == type)
{
add_existing_cell_to_cigar_record(dummy, len, type);
}
@@ -1379,7 +1094,7 @@ inline void add_cigar_record(char* seq, uint32_t len, Cigar_record* dummy, uint3
{
///add to existing cell, just increase length
///and add different bases
if(dummy->current_operation == type)
if((uint32_t)dummy->current_operation == type)
{
add_existing_cell_to_cigar_record_with_different_base(dummy, len, type, seq);
}
@@ -1394,7 +1109,7 @@ inline void add_cigar_record(char* seq, uint32_t len, Cigar_record* dummy, uint3
{
///add to existing cell, just increase length
///and add different bases
if(dummy->current_operation == type)
if((uint32_t)dummy->current_operation == type)
{
add_existing_cell_to_cigar_record_with_different_base(dummy, len, type, seq);
}
@@ -1418,7 +1133,7 @@ inline void add_cigar_record(char* seq, uint32_t len, Cigar_record* dummy, uint3
**/
///add to existing cell, just increase length
///and add different bases
if(dummy->current_operation == type)
if((uint32_t)dummy->current_operation == type)
{
add_existing_cell_to_cigar_record_with_different_base(dummy, len, type, seq);
}
@@ -1431,21 +1146,10 @@ inline void add_cigar_record(char* seq, uint32_t len, Cigar_record* dummy, uint3
}
dummy->current_operation = type;
}
int verify_cigar_2(char* x, int x_len, char* y, int y_len, Cigar_record* cigar, int error);
/**********************for prefilter************************ */
void destory_k_mer_pos_list_alloc_prefilter(k_mer_pos_list_alloc* list);
void append_k_mer_pos_list_alloc_prefilter(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
uint64_t n_end_pos, uint8_t n_direction, UC_Read* g_read, All_reads* R_INF, Correct_dumy* dumy);
/**********************for prefilter************************ */
int verify_single_window(long long x_start, long long x_end,
long long overlap_x_s, long long overlap_y_s, int x_id,