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DP

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This commit is contained in:
Haoyu Cheng
2019-09-07 21:25:11 -04:00
parent b57923d050
commit d6c6a1fa11
3 changed files with 660 additions and 2 deletions
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Correct.h
+75
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@@ -76,6 +76,30 @@ typedef struct
SnpStats;
#define Get_DP_Backtrack_Column(matrix, i) (matrix.backtrack + matrix.snp_num * i)
#define Get_DP_Backtrack_Column_Length(matrix, i) (matrix.snp_num)
typedef struct
{
// uint32_t snp_size;
// uint32_t snp_num;
// uint32_t* max;
// uint32_t* colum_len;
// uint32_t* colum;
// uint32_t matrix_size;
uint32_t snp_num;
uint32_t* max;
uint32_t snp_size;
uint32_t* backtrack_length;
uint32_t* backtrack;
uint32_t backtrack_size;
}
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)
@@ -100,6 +124,8 @@ typedef struct
SnpStats* snp_stat;
SnpStats result_stat;
uint32_t snp_stat_size;
DP_matrix dp;
}
haplotype_evdience_alloc;
@@ -263,6 +289,40 @@ inline void SetSnpMatrix(haplotype_evdience_alloc* h, long long snp_num, long lo
}
inline void init_DP_matrix(DP_matrix* dp, int32_t snp_num)
{
// if(snp_num + 1 > dp->snp_size)
// {
// dp->snp_size = snp_num + 1;
// dp->colum_len = (uint32_t*)realloc(dp->colum_len, dp->snp_size);
// dp->max = (uint32_t*)realloc(dp->max, dp->snp_size);
// }
// dp->snp_num = snp_num;
// if(snp_num > 0)
// {
// dp->colum_len[0] = 0;
// }
// dp->matrix_size = 0;
if(snp_num > dp->snp_size)
{
dp->snp_size = snp_num;
dp->max = (uint32_t*)realloc(dp->max, dp->snp_size * sizeof(uint32_t));
dp->backtrack_length = (uint32_t*)realloc(dp->backtrack_length, dp->snp_size * sizeof(uint32_t));
dp->backtrack_size = snp_num*snp_num;
dp->backtrack = (uint32_t*)realloc(dp->backtrack, dp->backtrack_size * sizeof(uint32_t));
}
dp->snp_num = snp_num;
}
inline void InitHaplotypeEvdience(haplotype_evdience_alloc* h)
{
h->snp = 0;
@@ -280,6 +340,21 @@ inline void InitHaplotypeEvdience(haplotype_evdience_alloc* h)
h->size = 100;
h->list = (haplotype_evdience*)calloc(h->size, sizeof(haplotype_evdience));
memset(h->flag, 0, WINDOW * sizeof(uint32_t));
// h->dp.max = NULL;
// h->dp.colum = NULL;
// h->dp.colum_len = NULL;
// h->dp.matrix_size = 0;
// h->dp.snp_num = 0;
// h->dp.snp_size = 0;
h->dp.snp_num = 0;
h->dp.max = NULL;
h->dp.snp_size = 0;
h->dp.backtrack = NULL;
h->dp.backtrack_size = 0;
h->dp.backtrack_length = NULL;
}
inline void StarSubListHaplotypeEvdience(haplotype_evdience_alloc* h)