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fix bug for gen_contain_consensus_chain

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chhylp123
2023-10-22 13:23:27 -04:00
parent 281ae6ba89
commit 4ca8951f9d
12 changed files with 281 additions and 54 deletions
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151
Process_Read.cpp
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@@ -208,6 +208,157 @@ int load_All_reads(All_reads* r, char* read_file_name)
return 1;
}
void read_ma(ma_hit_t* x, FILE* fp)
{
int f_flag;
f_flag = fread(&(x->qns), sizeof(x->qns), 1, fp);
f_flag += fread(&(x->qe), sizeof(x->qe), 1, fp);
f_flag += fread(&(x->tn), sizeof(x->tn), 1, fp);
f_flag += fread(&(x->ts), sizeof(x->ts), 1, fp);
f_flag += fread(&(x->te), sizeof(x->te), 1, fp);
f_flag += fread(&(x->el), sizeof(x->el), 1, fp);
f_flag += fread(&(x->no_l_indel), sizeof(x->no_l_indel), 1, fp);
uint32_t t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->ml = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->rev = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->bl = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->del = t;
}
int append_All_reads(All_reads* r, char *idx, uint32_t id)
{
char *gfa_name = NULL; MALLOC(gfa_name, (strlen(idx)+100));
FILE *fp = NULL, *fpo = NULL;
sprintf(gfa_name, "%s.ec%u.bin", idx, id);
fp = fopen(gfa_name, "r");
if (!fp) {free(gfa_name); return 0;}
sprintf(gfa_name, "%s.ovlp%u.source.bin", idx, id);
fpo = fopen(gfa_name, "r");
if (!fpo) {free(gfa_name); fclose(fp); return 0;}
free(gfa_name);
int local_adapterLen, f_flag;
f_flag = fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != asm_opt.adapterLen) {
fprintf(stderr, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, asm_opt.adapterLen);
exit(1);
}
uint64_t index_size0, name_index_size0, total_reads0, total_reads_bases0, total_name_length0;
index_size0 = r->index_size;
total_reads0 = r->total_reads;
total_reads_bases0 = r->total_reads_bases;
total_name_length0 = r->total_name_length;
name_index_size0 = ((total_reads0)?(total_reads0+1):(0));///r->name_index_size;
f_flag += fread(&r->index_size, sizeof(r->index_size), 1, fp);
f_flag += fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
f_flag += fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
f_flag += fread(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
f_flag += fread(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
r->index_size += index_size0;
r->name_index_size += name_index_size0; if(name_index_size0) r->name_index_size--;
r->total_reads += total_reads0;
r->total_reads_bases += total_reads_bases0;
r->total_name_length += total_name_length0;
uint64_t i = 0, zero = 0, k;
REALLOC(r->N_site, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
f_flag += fread(&zero, sizeof(zero), 1, fp);
if (zero) {
r->N_site[i] = (uint64_t*)malloc(sizeof(uint64_t)*(zero + 1));
r->N_site[i][0] = zero;
if (r->N_site[i][0]) {
f_flag += fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
} else {
r->N_site[i] = NULL;
}
}
REALLOC(r->read_length, r->total_reads);
f_flag += fread(r->read_length + total_reads0, sizeof(uint64_t), r->total_reads-total_reads0, fp);
REALLOC(r->read_size, r->total_reads);
memcpy (r->read_size + total_reads0, r->read_length + total_reads0, sizeof(uint64_t)*(r->total_reads-total_reads0));
REALLOC(r->read_sperate, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
f_flag += fread(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
REALLOC(r->name, r->total_name_length);
f_flag += fread(r->name + total_name_length0, sizeof(char), r->total_name_length - total_name_length0, fp);
REALLOC(r->name_index, r->name_index_size); uint64_t sft = 0;
if(name_index_size0) sft = r->name_index[--name_index_size0];
// fprintf(stderr, "name_index_size0::%lu, total_reads0::%lu, sft::%lu\n", name_index_size0, total_reads0, sft);
f_flag += fread(r->name_index + name_index_size0, sizeof(uint64_t), r->name_index_size-name_index_size0, fp);
if(sft) {
for (i = name_index_size0; i < r->name_index_size; i++) r->name_index[i] += sft;
}
/****************************may have bugs********************************/
REALLOC(r->trio_flag, r->total_reads);
f_flag += fread(r->trio_flag + total_reads0, sizeof(uint8_t), r->total_reads - total_reads0, fp);
int hom_cov0 = asm_opt.hom_cov, het_cov0 = asm_opt.het_cov;
f_flag += fread(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp); asm_opt.hom_cov += hom_cov0;
f_flag += fread(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp); asm_opt.het_cov += het_cov0;
/****************************may have bugs********************************/
REALLOC(r->cigars, r->total_reads);
REALLOC(r->second_round_cigar, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
r->second_round_cigar[i].size = r->cigars[i].size = 0;
r->second_round_cigar[i].length = r->cigars[i].length = 0;
r->second_round_cigar[i].record = r->cigars[i].record = NULL;
r->second_round_cigar[i].lost_base_size = r->cigars[i].lost_base_size = 0;
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
}
///r->pb_regions = NULL;
REALLOC(r->paf, r->total_reads);
memset(r->paf+total_reads0, 0, sizeof((*(r->paf)))*(r->total_reads - total_reads0));
long long n_read; f_flag = fread(&n_read, sizeof(n_read), 1, fpo); ma_hit_t t;
for (i = total_reads0; i < r->total_reads; i++) {
f_flag += fread(&(r->paf[i].is_fully_corrected), sizeof(r->paf[i].is_fully_corrected), 1, fpo);
f_flag += fread(&(r->paf[i].is_abnormal), sizeof(r->paf[i].is_abnormal), 1, fpo);
f_flag += fread(&(r->paf[i].length), sizeof(r->paf[i].length), 1, fpo);
if(r->paf[i].length == 0) continue;
for (k = 0; k < r->paf[i].length; k++) read_ma(&t, fpo);
r->paf[i].length = 0;
}
REALLOC(r->reverse_paf, r->total_reads);
memset(r->reverse_paf+total_reads0, 0, sizeof((*(r->reverse_paf)))*(r->total_reads - total_reads0));
fclose(fp); fclose(fpo);
fprintf(stderr, "Reads has been loaded.\n");
return 1;
}
int destory_read_bin(All_reads* r)
{