mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-29 05:08:13 +08:00
DP
This commit is contained in:
Haoyu Cheng
+583
-1
@@ -4118,6 +4118,39 @@ void add_to_result_snp_vector(haplotype_evdience_alloc* hap, int8_t *new_vector,
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}
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int debug_add_to_result_snp_vector(haplotype_evdience_alloc* hap, int8_t *new_vector, int Len)
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{
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int8_t *r_vector = Get_Result_SNP_Vector((*hap));
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int j;
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for (j = 0; j < Len; j++)
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{
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if(r_vector[j] == -1)
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{
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if(new_vector[j] == 0)
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{
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hap->result_stat.occ_0++;
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r_vector[j] = new_vector[j];
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}
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else if(new_vector[j] == 1)
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{
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hap->result_stat.occ_1++;
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r_vector[j] = new_vector[j];
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}
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}
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else ///can debug here
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{
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if((new_vector[j] != -1 && new_vector[j] != 2 && new_vector[j] != r_vector[j]))
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{
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fprintf(stderr, "j: %d\n", j);
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return 0;
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}
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}
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}
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return 1;
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}
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int merge_snp_vectors_and_test(haplotype_evdience_alloc* hap, int diff_vector_ID)
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@@ -4187,6 +4220,8 @@ int generate_haplotypes(haplotype_evdience_alloc* hap)
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return 0;
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}
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qsort(hap->snp_stat, hap->available_snp, sizeof(SnpStats), cmp_snp_stats);
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///the hap->core_snp is used to find centriod
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@@ -4255,6 +4290,351 @@ int generate_haplotypes(haplotype_evdience_alloc* hap)
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}
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void print_snp_in_line(haplotype_evdience_alloc* hap)
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{
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int j, i;
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uint32_t* column;
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fprintf(stderr, "\n\n\n###########hap->available_snp: %d###########\n", hap->available_snp);
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for (j = 0; j < hap->available_snp; j++)
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{
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fprintf(stderr, "*********j: %d, site: %d, id: %d*********\n", j, hap->snp_stat[j].site, hap->snp_stat[j].id);
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fprintf(stderr, "type(0):\n");
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int vectorID = hap->snp_stat[j].id;
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int8_t* vector = Get_SNP_Vector((*hap), vectorID);
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 0)
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{
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fprintf(stderr, "%3d, ", i);
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}
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}
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fprintf(stderr, "\n");
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fprintf(stderr, "type(1):\n");
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 1)
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{
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fprintf(stderr, "%3d, ", i);
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}
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}
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fprintf(stderr, "\n");
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}
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fprintf(stderr, "***********************\n");
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for (i = 0; i < hap->dp.snp_num; i++)
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{
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fprintf(stderr, "hap->dp.max[%d]: %d, hap->dp.backtrack_length: %d\n", i, hap->dp.max[i], hap->dp.backtrack_length[i]);
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if(hap->dp.backtrack_length[i] != 0)
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{
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column = Get_DP_Backtrack_Column(hap->dp, i);
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for (j = 0; j < hap->dp.backtrack_length[i]; j++)
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{
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fprintf(stderr, "pre: %d,", column[j]);
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}
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fprintf(stderr, "\n");
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}
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}
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}
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int generate_haplotypes_DP(haplotype_evdience_alloc* hap, overlap_region_alloc* overlap_list, All_reads* R_INF)
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{
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int j, i;
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int vectorID, vectorID2;
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int diff_core_vector = 0;
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int diff_vector_ID = -1;
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int8_t *vector, *vector2;
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if(hap->available_snp == 0)
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{
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return 0;
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}
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/**
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fprintf(stderr, "*******\nhap->available_snp: %d\n", hap->available_snp);
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for (j = 0; j < hap->available_snp; j++)
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{
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fprintf(stderr, "site: %d, id: %d\n", hap->snp_stat[j].site, hap->snp_stat[j].id);
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}
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**/
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///if hap->available_snp == 1, the following codes would have bugs
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///filter snps that are highly likly false
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if(hap->available_snp > 1)
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{
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i = 0;
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///if a snp is very near to others, it should not be a real snp
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for (j = 0; j < hap->available_snp; j++)
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{
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if(j > 0 && j < hap->available_snp - 1)
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{
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if(hap->snp_stat[j].site != hap->snp_stat[j - 1].site + 1
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&&
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hap->snp_stat[j].site + 1 != hap->snp_stat[j + 1].site)
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{
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hap->snp_stat[i] = hap->snp_stat[j];
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i++;
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}
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}
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else if(j == 0)
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{
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if(hap->snp_stat[j].site + 1 != hap->snp_stat[j + 1].site)
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{
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hap->snp_stat[i] = hap->snp_stat[j];
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i++;
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}
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}
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else
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{
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if(hap->snp_stat[j].site != hap->snp_stat[j - 1].site + 1)
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{
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hap->snp_stat[i] = hap->snp_stat[j];
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i++;
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}
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}
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}
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hap->available_snp = i;
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}
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int flag;
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long long overlap_length, total_read, unuseful_read;
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total_read = unuseful_read = 0;
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///check if any read may be conflict with others
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for (i = 0; i < overlap_list->length; i++)
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{
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overlap_length = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
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if (overlap_length * OVERLAP_THRESHOLD <= overlap_list->list[i].align_length)
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{
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total_read++;
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flag = -1;
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for (j = 0; j < hap->available_snp; j++)
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{
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vectorID = hap->snp_stat[j].id;
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vector = Get_SNP_Vector((*hap), vectorID);
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if(vector[i] != 2 && flag == 2)
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{
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unuseful_read++;
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flag = 3;
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break;
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}
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if(vector[i] == 2)
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{
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flag = 2;
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}
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}
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if(flag == 3)
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{
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for (j = 0; j < hap->available_snp; j++)
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{
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vectorID = hap->snp_stat[j].id;
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vector = Get_SNP_Vector((*hap), vectorID);
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vector[i] = 2;
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}
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}
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}
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}
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/*******************************DP********************************/
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init_DP_matrix(&(hap->dp), hap->available_snp);
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long long equal_best = 0;
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uint32_t* column;
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long long column_length;
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for (i = 0; i < hap->available_snp; i++)
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{
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///vector of snp i
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vectorID = hap->snp_stat[i].id;
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vector = Get_SNP_Vector((*hap), vectorID);
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hap->dp.max[i] = 1;
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hap->dp.backtrack_length[i] = 0;
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equal_best = 0;
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column = Get_DP_Backtrack_Column(hap->dp, i);
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column_length = Get_DP_Backtrack_Column_Length(hap->dp, i);
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for (j = 0; j < i; j++)
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{
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///vector of snp j
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vectorID2 = hap->snp_stat[j].id;
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vector2 = Get_SNP_Vector((*hap), vectorID2);
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///vector is compatible with vector2
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if(calculate_distance_snp_vector(vector, vector2, Get_SNP_Vector_Length((*hap))) == 0)
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{
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if(hap->dp.max[i] < hap->dp.max[j] + 1)
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{
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hap->dp.max[i] = hap->dp.max[j] + 1;
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column[0] = j;
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equal_best = 1;
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}
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else if(hap->dp.max[i] == hap->dp.max[j] + 1)
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{
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column[equal_best] = j;
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equal_best++;
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}
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}
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}
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hap->dp.backtrack_length[i] = equal_best;
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}
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/*******************************DP********************************/
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/**
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vector = Get_Result_SNP_Vector((*hap));
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memset(vector, -1, Get_SNP_Vector_Length((*hap)));
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vector = Get_Result_SNP_Vector((*hap));
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for (i = 0; i < hap->available_snp; i++)
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{
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if(hap->dp.max[i] > 1)
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{
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vector = Get_Result_SNP_Vector((*hap));
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memset(vector, -1, Get_SNP_Vector_Length((*hap)));
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if(hap->dp.backtrack_length[i] < 1)
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{
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fprintf(stderr, "error\n");
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}
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int debug_i = i;
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int round = hap->dp.max[i];
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while (hap->dp.max[debug_i] != 1)
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{
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vectorID2 = hap->snp_stat[debug_i].id;
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vector2 = Get_SNP_Vector((*hap), vectorID2);
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if(debug_add_to_result_snp_vector(hap, vector2, Get_SNP_Vector_Length((*hap))) == 0)
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{
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fprintf(stderr, "debug_i: %d\n", debug_i);
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print_snp_in_line(hap);
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}
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if(hap->dp.max[debug_i] != round)
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{
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fprintf(stderr, "hahah\n");
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}
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debug_i = hap->dp.backtrack_length[0];
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round--;
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}
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}
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}
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vector = Get_Result_SNP_Vector((*hap));
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memset(vector, -1, Get_SNP_Vector_Length((*hap)));
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if(hap->available_snp > 4)
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{
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fprintf(stderr, "\n\n\n###########hap->available_snp: %d###########\n", hap->available_snp);
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for (j = 0; j < hap->available_snp; j++)
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{
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fprintf(stderr, "*********site: %d, id: %d*********\n", hap->snp_stat[j].site, hap->snp_stat[j].id);
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fprintf(stderr, "type(0):\n");
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int vectorID = hap->snp_stat[j].id;
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int8_t* vector = Get_SNP_Vector((*hap), vectorID);
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 0)
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{
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fprintf(stderr, "%3d, ", i);
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}
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}
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fprintf(stderr, "\n");
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fprintf(stderr, "type(1):\n");
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 1)
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{
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fprintf(stderr, "%3d, ", i);
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}
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}
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fprintf(stderr, "\n");
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}
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fprintf(stderr, "***********************\n");
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for (i = 0; i < hap->dp.snp_num; i++)
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{
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fprintf(stderr, "hap->dp.max[%d]: %d, hap->dp.backtrack_length: %d\n", i, hap->dp.max[i], hap->dp.backtrack_length[i]);
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if(hap->dp.backtrack_length[i] != 0)
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{
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column = Get_DP_Backtrack_Column(hap->dp, i);
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for (j = 0; j < hap->dp.backtrack_length[i]; j++)
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{
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fprintf(stderr, "pre: %d,", column[j]);
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}
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fprintf(stderr, "\n");
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}
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}
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}
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**/
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/**
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fprintf(stderr, "overlap_list->length: %u, total_read: %u, unuseful_read: %u\n", overlap_list->length, total_read, unuseful_read);
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for (i = 0; i < overlap_list->length; i++)
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{
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overlap_length = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
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if (overlap_length * OVERLAP_THRESHOLD <= overlap_list->list[i].align_length)
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{
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total_read++;
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flag = -1;
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for (j = 0; j < hap->available_snp; j++)
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{
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vectorID = hap->snp_stat[j].id;
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vector = Get_SNP_Vector((*hap), vectorID);
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if(vector[i] != 2 && flag == 2)
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{
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fprintf(stderr, "hahahah\n");
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break;
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}
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if(vector[i] == 2)
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{
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flag = 2;
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}
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}
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}
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}
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**/
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return 0;
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}
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void print_Haplotype(haplotype_evdience_alloc* hap, overlap_region_alloc* overlap_list, All_reads* R_INF)
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{
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int j, i;
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@@ -4399,6 +4779,204 @@ void print_Haplotype(haplotype_evdience_alloc* hap, overlap_region_alloc* overla
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}
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void debug_near_snp(overlap_region_alloc* overlap_list, All_reads* R_INF,
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UC_Read* g_read, Correct_dumy* dumy, haplotype_evdience_alloc* hap)
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{
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int i, j, overlap_length, window_start, window_end, flag;
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long long window_num = (g_read->length + WINDOW - 1) / WINDOW;
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int total_read = 0;
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int unuseful_read = 0;
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for (i = 0; i < overlap_list->length; i++)
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{
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int flag = -1;
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overlap_length = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
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if (overlap_length * OVERLAP_THRESHOLD <= overlap_list->list[i].align_length)
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{
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total_read++;
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for (j = 0; j < hap->available_snp; j++)
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{
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int vectorID = hap->snp_stat[j].id;
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int8_t* vector = Get_SNP_Vector((*hap), vectorID);
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if(vector[i] != 2 && flag == 2)
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{
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unuseful_read++;
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break;
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}
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if(vector[i] == 2)
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{
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flag = 2;
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}
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}
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}
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}
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for (j = 1; j < hap->available_snp; j++)
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{
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if(hap->snp_stat[j].site <= hap->snp_stat[j - 1].site)
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{
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fprintf(stderr, "error\n");
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}
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}
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for (j = 0; j < hap->available_snp; j++)
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{
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fprintf(stderr, "\n\nsite: %d, score: %d\n", hap->snp_stat[j].site, hap->snp_stat[j].score );
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if((j>0 && hap->snp_stat[j].site == hap->snp_stat[j - 1].site + 1)
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||
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(j < hap->available_snp - 1 && hap->snp_stat[j].site + 1 == hap->snp_stat[j + 1].site))
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{
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fprintf(stderr, "x_name: %.*s\n",
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Get_NAME_LENGTH((*R_INF), overlap_list->list[0].x_id), Get_NAME((*R_INF),overlap_list->list[0].x_id));
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int vectorID = hap->snp_stat[j].id;
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int8_t* vector = Get_SNP_Vector((*hap), vectorID);
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 0)
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{
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fprintf(stderr, "type: %d, ID: %d\n", vector[i], i);
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}
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}
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for (i = 0; i < hap->overlap; i++)
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{
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if(vector[i] == 1)
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{
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fprintf(stderr, "type: %d, ID: %d, %.*s\n",
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vector[i], i,
|
||||
Get_NAME_LENGTH((*R_INF), overlap_list->list[i].y_id), Get_NAME((*R_INF),overlap_list->list[i].y_id));
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
window_start = 0;
|
||||
window_end = WINDOW - 1;
|
||||
if (window_end >= g_read->length)
|
||||
{
|
||||
window_end = g_read->length - 1;
|
||||
}
|
||||
long long ijk;
|
||||
for (ijk = 0; ijk < window_num; ijk++)
|
||||
{
|
||||
|
||||
|
||||
if(hap->snp_stat[j].site <= window_end && hap->snp_stat[j].site >= window_start)
|
||||
{
|
||||
fprintf(stderr, "winID: %d, winNum: %d, window_start: %d, window_end: %d\n",
|
||||
ijk, window_num, window_start, window_end);
|
||||
|
||||
dumy->length = 0;
|
||||
dumy->lengthNT = 0;
|
||||
///flag返回的是重叠数量
|
||||
///dumy->length返回的是有效完全重叠的数量
|
||||
///dumy->lengthNT返回的是有效不完全重叠的数量
|
||||
///return overlaps that is overlaped with [window_start, window_end]
|
||||
flag = get_available_interval(window_start, window_end, overlap_list, dumy);
|
||||
switch (flag)
|
||||
{
|
||||
case 1: ///找到匹配
|
||||
break;
|
||||
case 0: ///没找到匹配
|
||||
break;
|
||||
case -2: ///下一个window也不会存在匹配, 直接跳出
|
||||
i = window_num;
|
||||
break;
|
||||
}
|
||||
|
||||
|
||||
for (i = 0; i < dumy->length; i++)
|
||||
{
|
||||
///这个是那个overlap的ID，而不是overlap里对应窗口的ID
|
||||
int overlapID = dumy->overlapID[i];
|
||||
|
||||
///overlap_list->list[overlapID].x_pos_s is the begining of the whole overlap
|
||||
int correct_x_pos_s = (overlap_list->list[overlapID].x_pos_s / WINDOW) * WINDOW;
|
||||
///window_start is the begining of this window in the whole x_read
|
||||
int windowID = (window_start - correct_x_pos_s) / WINDOW;
|
||||
|
||||
///如果这个window不匹配，跳过
|
||||
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
if(vector[overlapID] == 1)
|
||||
{
|
||||
fprintf(stderr, "overlapID: %d, x_strat: %d, x_end: %d, y_start: %d, y_end: %d\n",
|
||||
overlapID,
|
||||
overlap_list->list[overlapID].w_list[windowID].x_start,
|
||||
overlap_list->list[overlapID].w_list[windowID].x_end,
|
||||
overlap_list->list[overlapID].w_list[windowID].y_start,
|
||||
overlap_list->list[overlapID].w_list[windowID].y_end);
|
||||
|
||||
recover_UC_Read_sub_region(dumy->overlap_region, overlap_list->list[overlapID].w_list[windowID].y_start,
|
||||
overlap_list->list[overlapID].w_list[windowID].y_end -overlap_list->list[overlapID].w_list[windowID].y_start + 1,
|
||||
overlap_list->list[overlapID].y_pos_strand,
|
||||
R_INF, overlap_list->list[overlapID].y_id);
|
||||
|
||||
char* x_string = g_read->seq + overlap_list->list[overlapID].w_list[windowID].x_start;
|
||||
char* y_string = dumy->overlap_region;
|
||||
|
||||
fprintf(stderr, "x_string: \n%.*s\n",
|
||||
overlap_list->list[overlapID].w_list[windowID].x_end - overlap_list->list[overlapID].w_list[windowID].x_start + 1,
|
||||
x_string);
|
||||
|
||||
fprintf(stderr, "y_string: \n%.*s\n",
|
||||
overlap_list->list[overlapID].w_list[windowID].y_end - overlap_list->list[overlapID].w_list[windowID].y_start + 1,
|
||||
y_string);
|
||||
|
||||
|
||||
int haha_i = 0;
|
||||
|
||||
for (haha_i = 0; haha_i < overlap_list->list[overlapID].w_list[windowID].cigar.length; haha_i++)
|
||||
{
|
||||
fprintf(stderr, "oper: %d, len: %d\n",
|
||||
overlap_list->list[overlapID].w_list[windowID].cigar.C_C[haha_i],
|
||||
overlap_list->list[overlapID].w_list[windowID].cigar.C_L[haha_i]
|
||||
);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
window_start = window_start + WINDOW;
|
||||
window_end = window_end + WINDOW;
|
||||
if (window_end >= g_read->length)
|
||||
{
|
||||
window_end = g_read->length - 1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
fprintf(stderr, "total_read: %d, unuseful_read: %d\n", total_read, unuseful_read);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
void partition_overlaps(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
UC_Read* g_read, Correct_dumy* dumy, haplotype_evdience_alloc* hap)
|
||||
{
|
||||
@@ -4503,7 +5081,10 @@ void partition_overlaps(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
|
||||
///debug_snp_matrix(hap);
|
||||
|
||||
qsort(hap->snp_stat, hap->available_snp, sizeof(SnpStats), cmp_snp_stats);
|
||||
generate_haplotypes_DP(hap, overlap_list, R_INF);
|
||||
|
||||
|
||||
///debug_near_snp(overlap_list, R_INF, g_read, dumy, hap);
|
||||
|
||||
///debug_snp_matrix(hap);
|
||||
|
||||
@@ -4521,6 +5102,7 @@ void partition_overlaps(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user