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better read phasing

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chhylp123
2021-12-07 22:47:52 -05:00
parent 1e2a9518e5
commit b640289b19
7 changed files with 552 additions and 197 deletions
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Correct.h
+103 -66
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@@ -229,7 +229,14 @@ DP_matrix;
#define Get_SNP_Martix_Size(matrix) (matrix.snp * matrix.overlap)
#define Get_SNP_Vector(matrix, i) (matrix.snp_matrix + matrix.overlap * i)
#define Get_SNP_Vector_Length(matrix) (matrix.overlap)
#define Get_Result_SNP_Vector(matrix) (matrix.snp_matrix + matrix.overlap*matrix.snp)
// #define Get_Result_SNP_Vector(matrix) (matrix.snp_matrix + matrix.overlap*matrix.snp)
#define Get_Result_SNP_Vector(matrix) (matrix.r_snp)
typedef struct
{
SnpStats* a;
size_t n,m;
}kv_SnpStats_t;
typedef struct
{
@@ -243,15 +250,22 @@ typedef struct
uint8_t flag[WINDOW_MAX_SIZE];
/****************************may have bugs********************************/
uint32_t available_snp;
uint32_t core_snp;
uint32_t snp;
uint32_t overlap;
int8_t* snp_matrix;
int8_t *snp_matrix;
uint32_t snp_matrix_size;
SnpStats* snp_stat;
int8_t *r_snp;
uint32_t r_snp_size;
SnpStats result_stat;
uint32_t snp_stat_size;
kv_SnpStats_t snp_stat;
uint32_t nn_snp;
kvec_t(uint64_t) snp_srt;
// SnpStats* snp_stat;
// uint32_t snp;
// uint32_t snp_stat_size;
// uint32_t available_snp;
DP_matrix dp;
}
@@ -341,9 +355,9 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
small_id = SNPs[i + 1];
if(hap->snp_stat[large_id].site - hap->snp_stat[current_id].site < distance
if(hap->snp_stat.a[large_id].site - hap->snp_stat.a[current_id].site < distance
||
hap->snp_stat[current_id].site - hap->snp_stat[small_id].site < distance)
hap->snp_stat.a[current_id].site - hap->snp_stat.a[small_id].site < distance)
{
(*nearsnp)++;
}
@@ -352,8 +366,8 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
(*non_nearsnps)++;
}
if(hap->snp_stat[current_id].site > hap->snp_stat[large_id].site ||
hap->snp_stat[current_id].site < hap->snp_stat[small_id].site)
if(hap->snp_stat.a[current_id].site > hap->snp_stat.a[large_id].site ||
hap->snp_stat.a[current_id].site < hap->snp_stat.a[small_id].site)
{
fprintf(stderr, "error\n");
}
@@ -362,7 +376,7 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
{
current_id= SNPs[i];
small_id = SNPs[i + 1];
if(hap->snp_stat[current_id].site - hap->snp_stat[small_id].site < distance)
if(hap->snp_stat.a[current_id].site - hap->snp_stat.a[small_id].site < distance)
{
(*nearsnp)++;
}
@@ -371,7 +385,7 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
(*non_nearsnps)++;
}
if(hap->snp_stat[current_id].site < hap->snp_stat[small_id].site)
if(hap->snp_stat.a[current_id].site < hap->snp_stat.a[small_id].site)
{
fprintf(stderr, "error\n");
}
@@ -380,7 +394,7 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
{
large_id = SNPs[i - 1];
current_id= SNPs[i];
if(hap->snp_stat[large_id].site - hap->snp_stat[current_id].site < distance)
if(hap->snp_stat.a[large_id].site - hap->snp_stat.a[current_id].site < distance)
{
(*nearsnp)++;
}
@@ -389,7 +403,7 @@ inline void count_nearby_snps(haplotype_evdience_alloc* hap, uint32_t* SNPs, int
(*non_nearsnps)++;
}
if(hap->snp_stat[current_id].site > hap->snp_stat[large_id].site)
if(hap->snp_stat.a[current_id].site > hap->snp_stat.a[large_id].site)
{
fprintf(stderr, "error\n");
}
@@ -632,46 +646,61 @@ UC_Read* g_read)
{
if(sub_length <= 0)
return;
long long i = 0;
h->snp_stat[h->available_snp].id = h->available_snp;
h->snp_stat[h->available_snp].occ_0 = 0;
h->snp_stat[h->available_snp].occ_1 = 0;
h->snp_stat[h->available_snp].occ_2 = 0;
h->snp_stat[h->available_snp].overlap_num = 0;
long long i = 0; SnpStats *p = NULL;
kv_pushp(SnpStats, h->snp_stat, &p);
h->snp_stat[h->available_snp].site = sub_list[0].site;
// h->snp_stat[h->available_snp].id = h->available_snp;
// h->snp_stat[h->available_snp].occ_0 = 0;
// h->snp_stat[h->available_snp].occ_1 = 0;
// h->snp_stat[h->available_snp].occ_2 = 0;
// h->snp_stat[h->available_snp].overlap_num = 0;
// h->snp_stat[h->available_snp].site = sub_list[0].site;
// 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);
// int8_t* vector = Get_SNP_Vector((*h), h->available_snp);
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);
int8_t* vector = Get_SNP_Vector((*h), h->available_snp);
p->id = h->snp_stat.n-1;
p->occ_0 = 0;
p->occ_1 = 0;
p->occ_2 = 0;
p->overlap_num = 0;
p->site = sub_list[0].site;
p->is_homopolymer = if_is_homopolymer_strict(p->site, g_read->seq, g_read->length);
int8_t* vector = Get_SNP_Vector((*h), p->id);
for (i = 0; i < sub_length; i++)
{
if(sub_list[i].type == 0)
{
vector[sub_list[i].overlapID] = 0;
h->snp_stat[h->available_snp].occ_0++;
// h->snp_stat[h->available_snp].occ_0++;
h->snp_stat.a[p->id].occ_0++;
}
else if(sub_list[i].type == 1 && sub_list[i].misBase == misBase)
{
vector[sub_list[i].overlapID] = 1;
h->snp_stat[h->available_snp].occ_1++;
// h->snp_stat[h->available_snp].occ_1++;
h->snp_stat.a[p->id].occ_1++;
}
else
{
vector[sub_list[i].overlapID] = 2;
h->snp_stat[h->available_snp].occ_2++;
// h->snp_stat[h->available_snp].occ_2++;
h->snp_stat.a[p->id].occ_2++;
}
h->snp_stat[h->available_snp].overlap_num++;
// h->snp_stat[h->available_snp].overlap_num++;
h->snp_stat.a[p->id].overlap_num++;
}
int new_occ_0 = h->snp_stat[h->available_snp].occ_0 + 1;
int new_occ_1 = h->snp_stat[h->available_snp].occ_1;
// int new_occ_0 = h->snp_stat[h->available_snp].occ_0 + 1;
// int new_occ_1 = h->snp_stat[h->available_snp].occ_1;
int new_occ_0 = h->snp_stat.a[p->id].occ_0 + 1;
int new_occ_1 = h->snp_stat.a[p->id].occ_1;
if(filter_snp(new_occ_0, new_occ_1, new_occ_0 + new_occ_1) == 0)
if(filter_snp(new_occ_0, new_occ_1, new_occ_0 + new_occ_1) == 0) ///Fix-attention:definitely wrong
{
h->snp_stat[h->available_snp].score = -1;
// h->snp_stat[h->available_snp].score = -1;
h->snp_stat.a[p->id].score = -1;
}
else
{
@@ -682,7 +711,7 @@ UC_Read* g_read)
consensus = consensus /((double)(new_occ_0 + new_occ_1));
///50% vs 50%
///50% vs 50%///Fix-attention:definitely wrong
if(new_occ_0 == new_occ_1)
{
consensus = consensus + 0.25;
@@ -707,12 +736,13 @@ UC_Read* g_read)
consensus= consensus*((double)(new_occ_0 + new_occ_1));
h->snp_stat[h->available_snp].score = consensus;
// h->snp_stat[h->available_snp].score = consensus;
h->snp_stat.a[p->id].score = consensus;
}
h->available_snp++;
// h->available_snp++;
}
@@ -760,32 +790,28 @@ inline int calculate_score(int new_occ_0, int new_occ_1)
return consensus;
}
inline void SetSnpMatrix(haplotype_evdience_alloc* h, long long snp_num, long long overlap_num)
inline void SetSnpMatrix(haplotype_evdience_alloc* h, uint32_t *nn_snp, uint64_t *overlap_num, int32_t set_matrix)
{
long long new_size = (snp_num + 1)* overlap_num;
if(nn_snp && overlap_num) {
kv_resize(SnpStats, h->snp_stat, *nn_snp);
h->snp_stat.n = 0; h->overlap = *overlap_num; h->core_snp = 0;
}
if(h->snp_matrix_size < new_size)
{
h->snp_matrix_size = new_size;
h->snp_matrix = (int8_t*)realloc(h->snp_matrix, h->snp_matrix_size);
if(set_matrix) {
uint64_t n_snp = nn_snp? *nn_snp:h->snp_stat.n;
uint64_t n_ovlp = overlap_num? *overlap_num:h->overlap;
uint64_t new_size = n_snp* n_ovlp;
if(h->snp_matrix_size < new_size) {
h->snp_matrix_size = new_size;
REALLOC(h->snp_matrix, h->snp_matrix_size);
}
memset(h->snp_matrix, -1, n_snp * n_ovlp);
if(h->r_snp_size < n_ovlp) {
h->r_snp_size = n_ovlp;
REALLOC(h->r_snp, h->r_snp_size);
}
}
if(h->snp_stat_size < snp_num)
{
h->snp_stat_size = snp_num;
h->snp_stat = (SnpStats*)realloc(h->snp_stat, h->snp_stat_size * sizeof(SnpStats));
}
///h->snp may be different with the number of snp vector
///since some snps have been filtered
h->snp = snp_num;
h->overlap = overlap_num;
h->available_snp = 0;
h->core_snp = 0;
memset(h->snp_matrix, -1, h->snp * h->overlap);
}
@@ -899,13 +925,19 @@ inline void init_DP_matrix(DP_matrix* dp, uint32_t snp_num)
inline void InitHaplotypeEvdience(haplotype_evdience_alloc* h)
{
h->snp = 0;
h->available_snp = 0;
h->overlap = 0;
h->snp_matrix_size = 0;
h->snp_stat_size = 0;
h->snp_matrix_size = 0;
h->snp_matrix = NULL;
h->snp_stat = NULL;
h->r_snp_size = 0;
h->r_snp = NULL;
kv_init(h->snp_stat);
kv_init(h->snp_srt);
h->nn_snp = 0;
// h->snp_stat = NULL;
// h->snp = 0;
// h->snp_stat_size = 0;
// h->available_snp = 0;
h->sub_list_start = 0;
@@ -954,8 +986,11 @@ inline void EndSubListHaplotypeEvdience(haplotype_evdience_alloc* h)
inline void destoryHaplotypeEvdience(haplotype_evdience_alloc* h)
{
free(h->list);
free(h->snp_stat);
// free(h->snp_stat);
kv_destroy(h->snp_stat);
kv_destroy(h->snp_srt);
free(h->snp_matrix);
free(h->r_snp);
free(h->dp.backtrack);
free(h->dp.max);
free(h->dp.max_for_sort);
@@ -968,7 +1003,9 @@ inline void destoryHaplotypeEvdience(haplotype_evdience_alloc* h)
inline void ResizeInitHaplotypeEvdience(haplotype_evdience_alloc* h)
{
h->snp = 0;
// h->snp = 0;
h->nn_snp = 0;
h->snp_stat.n = 0;
h->length = 0;
h->sub_list_start = 0;
h->sub_list_length = 0;