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improve speed

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This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
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103
Process_Read.cpp
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@@ -24,9 +24,15 @@ pthread_mutex_t i_doneMutex;
void init_All_reads(All_reads* r)
{
r->index_size = READ_INIT_NUMBER;
r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
r->index[0] = 0;
r->read = NULL;
/**********should remove**********/
///r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
///r->index[0] = 0;
///r->read = NULL;
/**********should remove**********/
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
r->read_sperate = NULL;
r->N_site = NULL;
r->total_reads_bases = 0;
@@ -50,11 +56,18 @@ void destory_All_reads(All_reads* r)
{
free(r->N_site[i]);
}
free(r->read_sperate[i]);
}
free(r->N_site);
free(r->read);
free(r->read_sperate);
///free(r->read);
free(r->name);
free(r->name_index);
free(r->read_length);
}
@@ -94,9 +107,22 @@ void write_All_reads(All_reads* r, char* read_file_name)
}
fwrite(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), fp);
/**********should remove**********/
///fwrite(r->index, sizeof(uint64_t), r->index_size, fp);
/**********should remove**********/
fwrite(r->read_length, sizeof(uint64_t), r->total_reads, fp);
/**********should remove**********/
///fwrite(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), fp);
/**********should remove**********/
for (i = 0; i < r->total_reads; i++)
{
fwrite(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
fwrite(r->name, sizeof(char), r->total_name_length, fp);
fwrite(r->index, sizeof(uint64_t), r->index_size, fp);
fwrite(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
@@ -152,15 +178,29 @@ int load_All_reads(All_reads* r, char* read_file_name)
}
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);
/**********should remove**********/
///r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
///fread(r->index, sizeof(uint64_t), r->index_size, fp);
/**********should remove**********/
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
fread(r->read_length, sizeof(uint64_t), r->total_reads, fp);
/**********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);
/**********should remove**********/
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
fread(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
fread(r->name, sizeof(char), r->total_name_length, fp);
r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
fread(r->index, sizeof(uint64_t), r->index_size, fp);
r->name_index = (uint64_t*)malloc(sizeof(uint64_t)*r->name_index_size);
fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
@@ -184,12 +224,20 @@ inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
if (r->index_size < r->total_reads + 2)
{
r->index_size = r->index_size * 2 + 2;
r->index = (uint64_t*)realloc(r->index,sizeof(uint64_t)*(r->index_size));
/**********should remove**********/
///r->index = (uint64_t*)realloc(r->index,sizeof(uint64_t)*(r->index_size));
/**********should remove**********/
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->index[r->total_reads] = r->index[r->total_reads-1] + read->l;
/**********should remove**********/
///r->index[r->total_reads] = r->index[r->total_reads-1] + read->l;
/**********should remove**********/
r->read_length[r->total_reads - 1] = read->l;
//r->index[r->total_reads] = r->index[r->total_reads-1] + read->l/4 + 1;
r->name_index[r->total_reads] = r->name_index[r->total_reads-1] + name->l;
@@ -197,11 +245,24 @@ inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
void malloc_All_reads(All_reads* r)
{
///必须加r->total_reads
r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
/**********should remove**********/
///r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
/**********should remove**********/
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
long long i = 0;
for (i = 0; i < r->total_reads; i++)
{
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
}
void destory_UC_Read(UC_Read* r)
@@ -369,6 +430,8 @@ void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID)
r->seq[R_INF->N_site[ID][i]] = 'N';
}
}
r->RID = ID;
}
@@ -426,7 +489,8 @@ 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)
{
(*N_site_lis) = (uint64_t*)malloc(sizeof(uint64_t)*(N_site_occ + 1));
@@ -442,7 +506,10 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
uint64_t dest_i = 0;
uint8_t tmp = 0;
uint8_t c = 0;
/**
fprintf(stderr, "src_l: %lld\n", src_l);
fflush(stderr);
**/
while (i + 4 <= src_l)
@@ -597,6 +664,8 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
read_batch->read[inner_i].ID = total_reads;
total_reads++;
///fprintf(stderr, "is_insert: %d\n", is_insert);
if (is_insert)
{
insert_read(&R_INF, &read_batch->read[inner_i].seq, &read_batch->read[inner_i].name);