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S/L index&reads

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This commit is contained in:
Haoyu Cheng
2019-05-16 21:14:50 -04:00
parent 3c5799aa1b
commit 17553e0a42
14 changed files with 297 additions and 5 deletions
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Process_Read.cpp
+126 -1
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@@ -41,6 +41,130 @@ void init_All_reads(All_reads* r)
}
void destory_All_reads(All_reads* r)
{
uint64_t i = 0;
for (i = 0; i < r->total_reads; i++)
{
if (r->N_site[i] != NULL)
{
free(r->N_site[i]);
}
}
free(r->N_site);
free(r->read);
free(r->name);
free(r->name_index);
}
void write_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Writing reads to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.bin", read_file_name);
FILE* fp = fopen(index_name, "w");
fwrite(&r->index_size, sizeof(r->index_size), 1, fp);
fwrite(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
fwrite(&r->total_reads, sizeof(r->total_reads), 1, fp);
fwrite(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
fwrite(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
uint64_t i = 0;
uint64_t zero = 0;
for (i = 0; i < r->total_reads; i++)
{
if (r->N_site[i] != NULL)
{
///这个实际上是N的个数
fwrite(&r->N_site[i][0], sizeof(r->N_site[i][0]), 1, fp);
if (r->N_site[i][0])
{
///r->N_site[i]这实际是个长为r->N_site[i][0]+1
///这里从r->N_site[i] + 1写入了r->N_site[i][0]个元素
fwrite(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
else
{
fwrite(&zero, sizeof(zero), 1, fp);
}
}
fwrite(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), 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);
free(index_name);
fclose(fp);
fprintf(stdout, "Reads has been written.\n");
}
void load_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Loading reads to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.bin", read_file_name);
FILE* fp = fopen(index_name, "r");
fread(&r->index_size, sizeof(r->index_size), 1, fp);
fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
fread(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
fread(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
uint64_t i = 0;
uint64_t zero = 0;
r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
fread(&zero, sizeof(zero), 1, fp);
if (zero)
{
r->N_site[i] = (uint64_t*)malloc(sizeof(uint64_t)*(zero + 1));
r->N_site[i][0] = zero;
if (r->N_site[i][0])
{
///r->N_site[i]这实际是个长为r->N_site[i][0]+1
///这里从r->N_site[i] + 1写入了r->N_site[i][0]个元素
fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
else
{
r->N_site[i] = NULL;
}
}
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);
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);
free(index_name);
fclose(fp);
fprintf(stdout, "Reads has been loaded.\n");
}
inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
{
@@ -68,7 +192,8 @@ 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));
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
}
void init_UC_Read(UC_Read* r)