xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-26 05:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

phasing

Browse Source
This commit is contained in:
Haoyu Cheng
2019-09-02 10:30:14 -04:00
parent 3c0c201cdf
commit d5327fe9ee
15 changed files with 3396 additions and 656 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Process_Read.cpp
+142
View File
@@ -186,6 +186,9 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
fread(r->read_length, sizeof(uint64_t), r->total_reads, fp);
r->read_size = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
memcpy (r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
/**********should remove**********/
///r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
///fread(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), fp);
@@ -205,6 +208,19 @@ int load_All_reads(All_reads* r, char* read_file_name)
fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
r->cigars[i].size = 0;
r->cigars[i].length = 0;
r->cigars[i].record = NULL;
r->cigars[i].lost_base_size = 0;
r->cigars[i].lost_base_length = 0;
r->cigars[i].lost_base = NULL;
}
free(index_name);
fclose(fp);
fprintf(stdout, "Reads has been loaded.\n");
@@ -246,6 +262,9 @@ inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
void malloc_All_reads(All_reads* r)
{
r->read_size = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
memcpy (r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
///必须加r->total_reads
/**********should remove**********/
///r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
@@ -257,7 +276,17 @@ void malloc_All_reads(All_reads* r)
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
}
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
r->cigars[i].size = 0;
r->cigars[i].length = 0;
r->cigars[i].record = NULL;
r->cigars[i].lost_base_size = 0;
r->cigars[i].lost_base_length = 0;
r->cigars[i].lost_base = NULL;
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
@@ -298,6 +327,119 @@ void init_UC_Read(UC_Read* r)
}
void recover_UC_Read_sub_region_begin_end
(char* r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID, int extra_begin, int extra_end)
{
long long readLen = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
long long i;
long long copyLen;
long long end_pos = start_pos + length - 1;
if (strand == 0)
{
i = start_pos;
copyLen = 0;
long long initLen = start_pos % 4;
if (initLen != 0)
{
memcpy(r, bit_t_seq_table[src[i>>2]] + initLen, 4 - initLen);
copyLen = copyLen + 4 - initLen;
i = i + copyLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
copyLen = copyLen + 4;
i = i + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= start_pos && R_INF->N_site[ID][i] <= end_pos)
{
r[R_INF->N_site[ID][i] - start_pos] = 'N';
}
else if(R_INF->N_site[ID][i] > end_pos)
{
break;
}
}
}
}
else
{
start_pos = readLen - start_pos - 1;
end_pos = readLen - end_pos - 1;
///start_pos > end_pos
i = start_pos;
copyLen = 0;
long long initLen = (start_pos + 1) % 4;
if (initLen != 0)
{
memcpy(r, bit_t_seq_table_rc[src[i>>2]] + 4 - initLen, initLen);
copyLen = copyLen + initLen;
i = i - initLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table_rc[src[i>>2]], 4);
copyLen = copyLen + 4;
i = i - 4;
}
if (R_INF->N_site[ID])
{
long long offset = readLen - start_pos - 1;
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= end_pos && R_INF->N_site[ID][i] <= start_pos)
{
r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
}
else if(R_INF->N_site[ID][i] > start_pos)
{
break;
}
}
}
}
}
void recover_UC_Read_sub_region(char* r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID)
{