int gehash_load(gehash_t * the_table, const char fname [])
{
int i, read_length;
char magic_chars[8];
magic_chars[7]=0;
the_table -> index_gap = 0;
FILE * fp = f_subr_open(fname, "rb");
if (!fp)
{
SUBREADprintf ("Table file `%s' is not found.\n", fname);
return 1;
}
fread(magic_chars,1,8,fp);
if(memcmp(magic_chars, "2subindx",8)!=0)
{
print_in_box(80,0,0,"");
print_in_box(80,0,0,"WARNING your reference index was built under an old version of subread");
print_in_box(80,0,0," package. Please rebuild the index for the reference genome.");
print_in_box(80,0,0,"");
}
if(memcmp(magic_chars+1, "subindx",7)==0)
{
if('1'==magic_chars[0])
the_table -> version_number = SUBINDEX_VER1;
else if('2'==magic_chars[0])
the_table -> version_number = SUBINDEX_VER2;
else assert(0);
if(SUBINDEX_VER2 == the_table -> version_number)
{
while(1)
{
short option_key, option_length;
fread(&option_key, 2, 1, fp);
if(!option_key) break;
fread(&option_length, 2, 1, fp);
if(option_key == SUBREAD_INDEX_OPTION_INDEX_GAP)
fread(&(the_table -> index_gap),2,1,fp);
else
fseek(fp, option_length, SEEK_CUR);
}
assert(the_table -> index_gap);
}
else if(SUBINDEX_VER1 == the_table -> version_number)
the_table -> index_gap = 3;
the_table -> current_items = load_int64(fp);
the_table -> buckets_number = load_int32(fp);
the_table -> buckets = (struct gehash_bucket * )malloc(sizeof(struct gehash_bucket) * the_table -> buckets_number);
if(!the_table -> buckets)
{
SUBREADputs(MESSAGE_OUT_OF_MEMORY);
return 1;
}
for (i=0; i<the_table -> buckets_number; i++)
{
struct gehash_bucket * current_bucket = &(the_table -> buckets[i]);
current_bucket -> current_items = load_int32(fp);
current_bucket -> space_size = load_int32(fp);
current_bucket -> space_size = current_bucket -> current_items;
current_bucket -> new_item_keys = (short *) malloc ( sizeof(short) * current_bucket -> space_size);
current_bucket -> item_values = (gehash_data_t *) malloc ( sizeof(gehash_data_t) * current_bucket -> space_size);
if(!(current_bucket -> new_item_keys&¤t_bucket -> item_values))
{
SUBREADputs(MESSAGE_OUT_OF_MEMORY);
return 1;
}
if(current_bucket -> current_items > 0)
{
read_length = fread(current_bucket -> new_item_keys, sizeof(short), current_bucket -> current_items, fp);
assert(read_length>0);
read_length = fread(current_bucket -> item_values, sizeof(gehash_data_t), current_bucket -> current_items, fp);
assert(read_length>0);
}
}
read_length = fread(&(the_table -> is_small_table), sizeof(char), 1, fp);
assert(read_length>0);
fclose(fp);
return 0;
}
else
{
fclose(fp);
the_table -> index_gap = 3;
fp = f_subr_open(fname, "rb");
the_table -> version_number = SUBINDEX_VER0;
the_table -> current_items = load_int64(fp);
the_table -> buckets_number = load_int32(fp);
the_table -> buckets = (struct gehash_bucket * )malloc(sizeof(struct gehash_bucket) * the_table -> buckets_number);
if(!the_table -> buckets)
{
SUBREADputs(MESSAGE_OUT_OF_MEMORY);
return 1;
}
for (i=0; i<the_table -> buckets_number; i++)
{
struct gehash_bucket * current_bucket = &(the_table -> buckets[i]);
current_bucket -> current_items = load_int32(fp);
current_bucket -> space_size = load_int32(fp);
current_bucket -> space_size = current_bucket -> current_items;
current_bucket -> item_keys = (gehash_key_t *) malloc ( sizeof(gehash_key_t) * current_bucket -> space_size);
current_bucket -> item_values = (gehash_data_t *) malloc ( sizeof(gehash_data_t) * current_bucket -> space_size);
if(!(current_bucket -> item_keys&¤t_bucket -> item_values))
{
SUBREADputs(MESSAGE_OUT_OF_MEMORY);
return 1;
}
if(current_bucket -> current_items > 0)
{
read_length = fread(current_bucket -> item_keys, sizeof(gehash_key_t), current_bucket -> current_items, fp);
assert(read_length>0);
read_length = fread(current_bucket -> item_values, sizeof(gehash_data_t), current_bucket -> current_items, fp);
assert(read_length>0);
}
}
read_length = fread(&(the_table -> is_small_table), sizeof(char), 1, fp);
assert(read_length>0);
fclose(fp);
return 0;
}
}
/*read the data contain in the file
*/
int32_t macsim_read(GenericReader_T* genreader,glu_item_t* item)
{
char data_var[LG_MAX_STRING_MACSIM];
uint32_t indice_data=0,
rep=EOF,
dimension=0;
uint8_t continuer=1;
TSP_sample_symbol_info_list_t ssi_list;
ssi_list=*genreader->ssi_list;
if(NULL!=genreader->handler->file)
{
/*TYPE_CHAR or TYPE_UCHAR is a string of LG_MAX_STRING_MACSIM length */
if( (TSP_TYPE_CHAR==ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].type)
|| (TSP_TYPE_UCHAR==ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].type) )
{
item->size=ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].dimension;
/*calculate the real dimension for the string symbol*/
dimension=ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].dimension/LG_MAX_STRING_MACSIM;
}
else
{
item->size=ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].dimension;
dimension=ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].dimension;
}
item->size*=tsp_type_size[ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].type];
while( continuer &&
(indice_data<dimension))
{
memset(data_var,'\0',LG_MAX_STRING_MACSIM);
/*read one data of the file*/
rep=read_data_file(genreader->handler->file,data_var);
if(EOF!=rep)
{
/*end of line*/
if(END_SAMPLE_SET==rep)
{
continuer=0;
}
/*load retrieve data in the raw value*/
switch(ssi_list.TSP_sample_symbol_info_list_t_val[item->provider_global_index].type)
{
case TSP_TYPE_DOUBLE :
load_double(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_FLOAT :
load_float(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_INT8 :
load_int8(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_INT16:
load_int16(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_INT32 :
load_int32(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_INT64 :
load_int64(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_UINT8:
load_uint8(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_UINT16:
load_uint16(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_UINT32:
load_uint32(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_UINT64:
load_uint64(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_CHAR:
load_char(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_UCHAR:
load_uchar(data_var,item->raw_value,indice_data);
break;
case TSP_TYPE_RAW:
load_type_raw(data_var,item->raw_value,indice_data);
break;
default:
break;
}
++indice_data;
}
else
{
continuer=0;
}
}
}
return(rep);
}