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prepare for integration with hifiasm

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This commit is contained in:
Heng Li
2020-03-26 11:33:52 -04:00
parent 60d94790a2
commit c3bbaa8a39
3 changed files with 38 additions and 157 deletions
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149
Process_Read.cpp
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@@ -81,7 +81,6 @@ void destory_All_reads(All_reads* r)
free(r->trio_flag);
}
void write_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stderr, "Writing reads to disk... \n");
@@ -112,9 +111,6 @@ void write_All_reads(All_reads* r, char* read_file_name)
{
fwrite(&zero, sizeof(zero), 1, fp);
}
}
fwrite(r->read_length, sizeof(uint64_t), r->total_reads, fp);
@@ -132,8 +128,6 @@ void write_All_reads(All_reads* r, char* read_file_name)
fprintf(stderr, "Reads has been written.\n");
}
int load_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stderr, "Loading reads from disk... \n");
@@ -164,7 +158,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
f_flag += fread(&zero, sizeof(zero), 1, fp);
if (zero)
@@ -233,32 +226,33 @@ int load_All_reads(All_reads* r, char* read_file_name)
return 1;
}
inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
void ha_insert_read_len(All_reads *r, int read_len, int name_len)
{
r->total_reads++;
r->total_reads_bases = r->total_reads_bases + read->l;
r->total_name_length = r->total_name_length + name->l;
r->total_reads_bases += (uint64_t)read_len;
r->total_name_length += (uint64_t)name_len;
///must +1
if (r->index_size < r->total_reads + 2)
{
// must +1
if (r->index_size < r->total_reads + 2) {
r->index_size = r->index_size * 2 + 2;
r->read_length = (uint64_t*)realloc(r->read_length,sizeof(uint64_t)*(r->index_size));
r->read_length = (uint64_t*)realloc(r->read_length, sizeof(uint64_t) * r->index_size);
r->name_index_size = r->name_index_size * 2 + 2;
r->name_index = (uint64_t*)realloc(r->name_index,sizeof(uint64_t)*(r->name_index_size));
r->name_index = (uint64_t*)realloc(r->name_index, sizeof(uint64_t) * r->name_index_size);
}
r->read_length[r->total_reads - 1] = read->l;
r->name_index[r->total_reads] = r->name_index[r->total_reads-1] + name->l;
r->read_length[r->total_reads - 1] = read_len;
r->name_index[r->total_reads] = r->name_index[r->total_reads - 1] + name_len;
}
static inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
{
ha_insert_read_len(r, read->l, name->l);
}
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);
memcpy(r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
long long i = 0;
@@ -313,7 +307,6 @@ void init_aux_table()
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]);
}
}
}
@@ -338,18 +331,12 @@ void init_UC_Read(UC_Read* r)
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]);
}
}
}
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)
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);
@@ -357,17 +344,11 @@ void recover_UC_Read_sub_region_begin_end
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)
@@ -376,8 +357,6 @@ void recover_UC_Read_sub_region_begin_end
copyLen = copyLen + 4 - initLen;
i = i + copyLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
@@ -385,7 +364,6 @@ void recover_UC_Read_sub_region_begin_end
i = i + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -400,17 +378,12 @@ void recover_UC_Read_sub_region_begin_end
}
}
}
}
else
{
start_pos = readLen - start_pos - 1;
end_pos = readLen - end_pos - 1;
///start_pos > end_pos
i = start_pos;
copyLen = 0;
@@ -436,7 +409,6 @@ void recover_UC_Read_sub_region_begin_end
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos)
{
r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
@@ -447,21 +419,11 @@ void recover_UC_Read_sub_region_begin_end
}
}
}
}
}
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)
{
long long readLen = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
@@ -471,7 +433,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
if (strand == 0)
{
i = start_pos;
copyLen = 0;
@@ -483,8 +444,7 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
copyLen = copyLen + 4 - initLen;
i = i + copyLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
@@ -492,7 +452,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
i = i + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -507,17 +466,12 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
}
}
}
}
else
{
start_pos = readLen - start_pos - 1;
end_pos = readLen - end_pos - 1;
///start_pos > end_pos
i = start_pos;
copyLen = 0;
@@ -543,7 +497,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos)
{
r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
@@ -554,11 +507,7 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
}
}
}
}
}
@@ -623,7 +572,6 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
index = index + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -631,11 +579,8 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
}
}
}
#define COMPRESS_BASE {c = seq_nt6_table[(uint8_t)src[i]];\
if (c >= 4)\
{\
@@ -647,7 +592,6 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
{
///N_site_lis saves the pos of all Ns in this read
///N_site_lis[0] is the number of Ns
if (N_site_occ)
@@ -666,10 +610,8 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
uint8_t tmp = 0;
uint8_t c = 0;
while (i + 4 <= src_l)
{
tmp = 0;
COMPRESS_BASE;
@@ -705,12 +647,8 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
dest[dest_i] = tmp;
dest_i++;
}
}
void open_file(gz_files* nfps, char* name)
{
nfps->fp = gzopen(name, "r");
@@ -722,7 +660,6 @@ void open_file(gz_files* nfps, char* name)
nfps->seq = kseq_init(nfps->fp);
}
void close_file(gz_files* nfps)
{
kseq_destroy(nfps->seq);
@@ -774,11 +711,9 @@ inline void exchage_kstring_t(kstring_t* a, kstring_t* b)
int get_read(kseq_t *s, int adapterLen)
{
int l;
///if ((l = kseq_read(seq)) >= 0)
if ((l = read_item()) >= 0)
{
exchage_kstring_t(&(fps.seq->comment), &s->comment);
exchage_kstring_t(&(fps.seq->name), &s->name);
exchage_kstring_t(&(fps.seq->qual), &s->qual);
@@ -801,15 +736,12 @@ int get_read(kseq_t *s, int adapterLen)
}
}
return 1;
}
else
{
return 0;
}
}
void init_R_buffer_block(R_buffer_block* curr_sub_block)
@@ -823,6 +755,7 @@ void clear_R_buffer()
RDB.all_read_end = 0;
RDB.num = 0;
}
void init_R_buffer(int thread_num)
{
RDB.all_read_end = 0;
@@ -841,13 +774,11 @@ void init_R_buffer(int thread_num)
}
void destory_R_buffer_block(R_buffer_block* curr_sub_block)
{
kseq_destroy(curr_sub_block->read);
}
void destory_R_buffer()
{
int i = 0;
@@ -858,7 +789,6 @@ void destory_R_buffer()
}
free(RDB.sub_block);
}
@@ -868,12 +798,8 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
int inner_i = 0;
int file_flag = 1;
while (inner_i<batch_read_size)
{
file_flag = get_read(&read_batch->read[inner_i], adapterLen);
if (file_flag == 1)
@@ -881,7 +807,6 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
read_batch->read[inner_i].ID = total_reads;
total_reads++;
if (is_insert)
{
insert_read(&R_INF, &read_batch->read[inner_i].seq,
@@ -903,14 +828,11 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
*return_file_flag = file_flag;
read_batch->num = inner_i;
}
inline void push_R_block(R_buffer_block* tmp_sub_block)
{
///only exchange pointers
kseq_t *k1;
k1 = RDB.sub_block[RDB.num].read;
@@ -940,29 +862,20 @@ inline void pop_R_block(R_buffer_block* curr_sub_block)
curr_sub_block->num = RDB.sub_block[RDB.num].num;
RDB.sub_block[RDB.num].num = 0;
}
void* input_reads_muti_threads(void* arg)
{
int is_insert = *((int*)arg);
total_reads = 0;
int file_flag = 1;
R_buffer_block tmp_buf;
init_R_buffer_block(&tmp_buf);
while (1)
{
load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert, asm_opt.adapterLen);
@@ -972,7 +885,6 @@ void* input_reads_muti_threads(void* arg)
break;
}
pthread_mutex_lock(&i_readinputMutex);
while (IS_FULL(RDB))
{
@@ -981,14 +893,12 @@ void* input_reads_muti_threads(void* arg)
pthread_cond_wait(&i_readinputflushCond, &i_readinputMutex);
}
push_R_block(&tmp_buf);
pthread_cond_signal(&i_readinputstallCond);
pthread_mutex_unlock(&i_readinputMutex);
}
pthread_mutex_lock(&i_readinputMutex);
RDB.all_read_end = 1;
pthread_cond_signal(&i_readinputstallCond); //important
@@ -999,34 +909,25 @@ void* input_reads_muti_threads(void* arg)
fprintf(stderr, "Reads #: %lu\n", (unsigned long)total_reads);
fprintf(stderr, "Bases #: %lu\n", (unsigned long)R_INF.total_reads_bases);
return NULL;
}
int get_reads_mul_thread(R_buffer_block* curr_sub_block)
{
pthread_mutex_lock(&i_readinputMutex);
while (IS_EMPTY(RDB) && RDB.all_read_end == 0)
{
pthread_cond_signal(&i_readinputflushCond);
pthread_cond_wait(&i_readinputstallCond, &i_readinputMutex);
}
if (!IS_EMPTY(RDB))
{
pop_R_block(curr_sub_block);
pthread_cond_signal(&i_readinputflushCond);
pthread_mutex_unlock(&i_readinputMutex);
return 1;
}
else
@@ -1039,17 +940,8 @@ int get_reads_mul_thread(R_buffer_block* curr_sub_block)
return 0;
}
}
void reverse_complement(char* pattern, uint64_t length)
{
uint64_t i = 0;
@@ -1069,11 +961,8 @@ void reverse_complement(char* pattern, uint64_t length)
{
pattern[end] = RC_CHAR(pattern[end]);
}
}
typedef struct {
char* tmp;
long long tmpSize;