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This commit is contained in:
Haoyu Cheng
2019-07-01 09:08:25 -04:00
parent 30161f1544
commit b553f3ac5e
17 changed files with 732 additions and 18 deletions
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Process_Read.cpp
+51
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@@ -204,6 +204,12 @@ void malloc_All_reads(All_reads* r)
}
void destory_UC_Read(UC_Read* r)
{
free(r->seq);
}
void init_UC_Read(UC_Read* r)
{
r->length = 0;
@@ -219,6 +225,11 @@ void init_UC_Read(UC_Read* r)
bit_t_seq_table[i][1] = s_H[((i >> 4)&(uint64_t)3)];
bit_t_seq_table[i][2] = s_H[((i >> 2)&(uint64_t)3)];
bit_t_seq_table[i][3] = s_H[(i&(uint64_t)3)];
bit_t_seq_table_rc[i][0] = RC_CHAR(bit_t_seq_table[i][3]);
bit_t_seq_table_rc[i][1] = RC_CHAR(bit_t_seq_table[i][2]);
bit_t_seq_table_rc[i][2] = RC_CHAR(bit_t_seq_table[i][1]);
bit_t_seq_table_rc[i][3] = RC_CHAR(bit_t_seq_table[i][0]);
}
}
@@ -256,6 +267,46 @@ void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID)
}
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)
{
r->size = r->length + 4;
r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
}
long long last_chr = r->length % 4;
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 <= R_INF->N_site[ID][0]; i++)
{
r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
}
}
}
#define COMPRESS_BASE {c = seq_nt6_table[src[i]];\