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#include "Index_Table.h"
const char* CHECK_SUM = "End_of_Index";
CIndex_Table::CIndex_Table(void)
{
initialization();
}
CIndex_Table::~CIndex_Table(void)
{
delete_index_table();
}
int CIndex_Table::initialization()
{
// this->capacity = 0;
this->size = 0;
this->chosenSeedId = 3;
this->uiSubDiffThreshold = 3;
this->uiRead_Length = 0;
this->bMapReadInColors = false;
this->pIndexTable = NULL;
this->pHashIndexTable = NULL;
this->pbaMaskedFlag = NULL;
return(0);
}
void CIndex_Table::delete_index_table(void)
{
delete [] this->pIndexTable;
delete this->pbaMaskedFlag;
delete this->pHashIndexTable;
this->initialization(); // pointer to NULL;
}
void CIndex_Table::printInfo(void) const
{
LOG_INFO("Info %d: Read length is %u with size %u\n",\
CONFIG_LOG, this->uiRead_Length, this->size);
if (this->bMapReadInColors) {
LOG_INFO("Info %d: This index table is for SOLiD reads. %s\n",\
CONFIG_LOG, BLANK_LINE);
} else {
LOG_INFO("Info %d: This index table is for Illumina reads. %s\n",\
CONFIG_LOG, BLANK_LINE);
}
}
// Save the index to a file with binary file. filePostfix should indicate which reference genome is preprocessed.
bool CIndex_Table::save_Hash_Table(FILE* fp) const
{
bool sucessfullySaveTable = true;
char colorReads = this->bMapReadInColors ? 'Y' : 'N';
// TODO: write the seed option into index
// int seedOption = this->chosenSeedId;
if (this->pIndexTable != NULL) {
printInfo();
fprintf(fp, "%u\n%u\n%u\n%c", this->chosenSeedId, this->uiRead_Length, this->size, colorReads);
// save hash table
sucessfullySaveTable = myFwrite((void*)this->pIndexTable, sizeof(CIndex_Type), this->size, fp);
if (!sucessfullySaveTable) ERR;
if (this->pHashIndexTable != NULL) {
fprintf(fp, "\n%u\n%u", \
this->pHashIndexTable->uiWindowSize, this->pHashIndexTable->uiSize);
// The Hash Index table has uiSize + 1 record
sucessfullySaveTable = myFwrite((void*)this->pHashIndexTable->aiIndexTable, \
sizeof(unsigned int), (this->pHashIndexTable->uiSize + 1), fp);
if (!sucessfullySaveTable) ERR;
} else {
ERR;
sucessfullySaveTable = false;
}
// Write math repeat flags
if (this->pbaRepeatRepresentativeFlag != NULL) {
fprintf(fp, "\n%u", this->pbaRepeatRepresentativeFlag->size);
sucessfullySaveTable = myFwrite((void*) this->pbaRepeatRepresentativeFlag->bflag,
sizeof(unsigned char), (this->pbaRepeatRepresentativeFlag->size / 8 + 1), fp);
if (!sucessfullySaveTable) ERR;
}
fprintf(fp, "\n%s\n", CHECK_SUM);
} else {
LOG_INFO("Info %d: The Index is empty\n", ERROR_LOG);
sucessfullySaveTable = false;
}
return(sucessfullySaveTable);
}
bool CIndex_Table::read_Hash_Table(FILE* fp)
{
bool sucessfullyReadTable = true;
// int seedOption = this->chosenSeedId;
if (fscanf(fp, "%u\n%u\n%u\n", \
&this->chosenSeedId, &this->uiRead_Length, &this->size) != 3) {
ERR; // Read hash table
}
// Get a character until Y or N, indicating this is the SOliD reads.
while (char c = (char)fgetc(fp)) { // This is a check sum of the correctness.
if (c == 'Y' || c == 'N') {
this->bMapReadInColors = (c == 'Y');
LOG_INFO("Info %d: Mapping SOLiD reads (Yes/No): %c%s\n", CONFIG_LOG, c, BLANK_LINE);
break;
}
}
LOG_INFO("Info %d: Anchor length: %u, Size: %u\n", CONFIG_LOG, this->uiRead_Length, this->size);
if (this->pIndexTable == NULL) {
this->pIndexTable = new CIndex_Type[this->size];
if (this->pIndexTable == NULL) ERR; // fail to new space for table
} else
LOG_INFO("Info %d: HashTable was not NULL\n", WARNING_LOG);
sucessfullyReadTable = myFread((void*)this->pIndexTable, sizeof(CIndex_Type), this->size, fp);
if (!sucessfullyReadTable) {
LOG_INFO("Info %d: Fail to read index.\n", ERROR_LOG);
delete this->pIndexTable;
this->pIndexTable = NULL;
return(!sucessfullyReadTable);
}
unsigned int uiWindowSize = 0, uiHashIndexTableSize = 0;
if (fscanf(fp, "\n%u\n%u", &(uiWindowSize), &(uiHashIndexTableSize)) <=0) {
ERR;
}
LOG_INFO("Info %d: Take the first %u bases for hashing(bucketing)\n", FINE_LOG, uiWindowSize);
if (uiHashIndexTableSize > 0 && uiHashIndexTableSize > 0) {
if (this->pHashIndexTable == NULL) {
this->pHashIndexTable = new CHashIndexT(uiHashIndexTableSize); //Note there are one more counter
}
if (this->pHashIndexTable == NULL) {
ERR; // Fail to new pHashIndexTable
return(!sucessfullyReadTable);
}
sucessfullyReadTable = myFread((void*)this->pHashIndexTable->aiIndexTable,\
sizeof(unsigned int), (this->pHashIndexTable->uiSize + 1), fp);
if (!sucessfullyReadTable) ERR;
} else {
ERR;
}
// Read math repeat flags
unsigned int numOfFlags = 0;
if (fscanf(fp, "\n%u", &(numOfFlags)) <=0 ) {
ERR;
}
if (this->pbaRepeatRepresentativeFlag == NULL) {
this->pbaRepeatRepresentativeFlag = new CboolFlagArray(numOfFlags);
}
sucessfullyReadTable = myFread((void*)this->pbaRepeatRepresentativeFlag->bflag,
sizeof(unsigned char), (this->pbaRepeatRepresentativeFlag->size / 8 + 1), fp);
if (!sucessfullyReadTable || !assertFile(fp, CHECK_SUM)) {
ERR;
}
return(sucessfullyReadTable);
}
string default_index_path(string filePostfix, bool bColorReads,\
unsigned int seedOption, unsigned int uiReadLength)
{
char fileName[MAX_LINE];
const char* colorReads = bColorReads ? "SOLiD" : "Illumina";
sprintf(fileName, "%u_%u_%s_%s_v2.index", \
uiReadLength, seedOption, colorReads, filePostfix.c_str());
return(string(fileName));
}
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