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checkpoint for scaffolding

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chhylp123
2023-09-15 12:58:34 -04:00
parent 858b95a3bb
commit c7685e6f19
8 changed files with 1735 additions and 98 deletions
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91
Process_Read.cpp
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@@ -541,31 +541,27 @@ void recover_UC_Read(UC_Read* r, const All_reads *R_INF, uint64_t ID)
r->length = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
if (r->length + 4 > r->size)
{
if (r->length + 4 > r->size) {
r->size = r->length + 4;
r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
}
uint64_t i = 0;
while ((long long)i < r->length)
{
memcpy(r->seq+i, bit_t_seq_table[src[i>>2]], 4);
i = i + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
{
r->seq[R_INF->N_site[ID][i]] = 'N';
if(src) {
while ((long long)i < r->length) {
memcpy(r->seq+i, bit_t_seq_table[src[i>>2]], 4);
i = i + 4;
}
if (R_INF->N_site[ID]) {
for (i = 1; i <= R_INF->N_site[ID][0]; i++) r->seq[R_INF->N_site[ID][i]] = 'N';
}
} else {///N
memset(r->seq, 'N', r->length);
}
r->RID = ID;
r->RID = ID;
}
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
@@ -573,8 +569,7 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
r->length = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
if (r->length + 4 > r->size)
{
if (r->length + 4 > r->size) {
r->size = r->length + 4;
r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
}
@@ -583,27 +578,29 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
long long i = r->length / 4 - 1 + (last_chr != 0);
long long index = 0;
if(last_chr!=0)
{
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]] + 4 - last_chr, last_chr);
index = last_chr;
i--;
}
while (i >= 0)
{
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]], 4);
i--;
index = index + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
if(src) {
if(last_chr!=0) {
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]] + 4 - last_chr, last_chr);
index = last_chr;
i--;
}
while (i >= 0) {
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]], 4);
i--;
index = index + 4;
}
if (R_INF->N_site[ID]) {
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++) {
r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
}
}
} else {///N
memset(r->seq, 'N', r->length);
}
}
#define COMPRESS_BASE {c = seq_nt6_table[(uint8_t)src[i]];\
@@ -1893,4 +1890,24 @@ int64_t load_compress_base_disk(FILE *fp, uint64_t *ul_rid, char *dest, uint32_t
des_i += tailLen; src_i += tailLen;
}
return 1;
}
scaf_res_t *init_scaf_res_t(uint32_t n)
{
scaf_res_t *p = NULL; CALLOC(p, 1);
p->n = p->m = n; CALLOC(p->a, n);
return p;
}
void destroy_scaf_res_t(scaf_res_t *p)
{
if(p) {
uint32_t k;
for (k = 0; k < p->m; k++) {
free(p->a[k].N_site.a); free(p->a[k].r_base.a); free(p->a[k].bb.a);
}
free(p->a);
free(p);
}
}