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#include "PairedReadsSet.h"
CPairedReadsSet::CPairedReadsSet()
{
this->initialization();
}
CPairedReadsSet::CPairedReadsSet(const char* InputFile, const char* fileFormat,\
unsigned int expReadStrLineLength, bool in5to3cat3to5Format,\
unsigned int allowedNumOfNinRead, unsigned int readStartIndex)
{
bool bDiscardReadsWN = (allowedNumOfNinRead == 0);
this->initialization();
// TODO rename the uiRead_Length variable to proper name
if (expReadStrLineLength % 2 == 1) {
this->uiRead_Length = (expReadStrLineLength + 1) / 2;
} else { // The uiRead_Length length is the length of each end; not the total read length
this->uiRead_Length = expReadStrLineLength / 2;
}
this->in5to3cat3to5Format = in5to3cat3to5Format;
unsigned int uiCapacity = BUFFERED_READS_SIZE ;
this->F_Reads = new CReadInBitsSet(uiCapacity, this->uiRead_Length);
this->F_Reads->bDiscardReadWithN = bDiscardReadsWN;
this->F_Reads->allowedNumOfNinRead = allowedNumOfNinRead;
this->R_Reads = new CReadInBitsSet(uiCapacity, this->uiRead_Length);
this->R_Reads->bDiscardReadWithN = bDiscardReadsWN;
this->R_Reads->allowedNumOfNinRead = allowedNumOfNinRead;
myStrCpy(this->InputFile, InputFile, FILENAME_MAX);
myStrCpy(this->F_Reads->InputFile, InputFile, FILENAME_MAX);
// chExtName(this->F_Reads->InputFile, "_F");
myStrCpy(this->R_Reads->InputFile, InputFile, FILENAME_MAX);
// chExtName(this->R_Reads->InputFile, "_R");
// The length will be changed for long read with odd bases
this->parser.caNextRead[expReadStrLineLength] = '\0';
this->openAFileReady2GetRead(InputFile, fileFormat, expReadStrLineLength, bDiscardReadsWN);
// Haven't seen csfasta has QUAL file in the 5'-3'3'-5' form
}
CPairedReadsSet::CPairedReadsSet(unsigned int Capacity, unsigned int uiReadLength)
{
this->F_Reads = new CReadInBitsSet(Capacity, uiReadLength);
this->R_Reads = new CReadInBitsSet(Capacity, uiReadLength);
}
CPairedReadsSet::~CPairedReadsSet(void)
{
delete this->F_Reads;
delete this->R_Reads;
delete this->pQualScoresF;
delete this->pQualScoresR;
}
unsigned int CPairedReadsSet::openAFileReady2GetRead\
(const char* InputFile, const char* fileFormat, unsigned int uiExpReadsStrLength, bool bDiscardReadsWN)
{
// const unsigned int uiExpReadsStrLength = this->uiRead_Length * 2;
const unsigned int uiReadStartIndex = 0; // In this format, no base can be removed from the 5' end
myStrCpy(this->InputFile, InputFile, FILENAME_MAX);
this->cFileType = this->parser.openAFileReady2GetRead\
(InputFile, fileFormat, uiReadStartIndex, uiExpReadsStrLength, bDiscardReadsWN);
bool bGetQScores = (this->cFileType == 'Q' || this->cFileType == 'q');
bool bSOLiDReadFormat = (this->cFileType == 'S' || this->cFileType == 'Q');
if ( this->cFileType == 'N') {
return(1);
} else if (bSOLiDReadFormat) {
string msg1 = "Currently, we don't know any SOLiD pair-end reads in the format,";
string msg2 = "that concatenate forward and backward trend together";
LOG_INFO("\nInfo %d: %s\n%s\n", WARNING_LOG, msg1.c_str(), msg2.c_str());
return(1);
} else if (bGetQScores) {
this->F_Reads->pQualScores = new CReadsQualScores(this->uiRead_Length, BUFFERED_READS_SIZE);
this->R_Reads->pQualScores = new CReadsQualScores(this->uiRead_Length, BUFFERED_READS_SIZE);
}
// For csfasta reads, new the quality score space when QUAL files exists
this->F_Reads->clear(BUFFERED_READS_SIZE);
this->R_Reads->clear(BUFFERED_READS_SIZE);
return(BUFFERED_READS_SIZE);
}
void CPairedReadsSet::clearReads(void)
{
this->F_Reads->clear(BUFFERED_READS_SIZE);
this->R_Reads->clear(BUFFERED_READS_SIZE);
}
void CPairedReadsSet::ignoreQScores(void)
{
this->F_Reads->ignoreQScores();
this->R_Reads->ignoreQScores();
}
void CPairedReadsSet::removeExtraTags(void)
{
for (unsigned int i = (unsigned int)(F_Reads->pReadsID->size()); i > this->uiNo_of_Reads; i--) {
this->F_Reads->pReadsID->pop_back(); // remove extra tags
this->R_Reads->pReadsID->pop_back(); // remove extra tags
}
}
void CPairedReadsSet::getQualityScoresFromQUAL(void)
{
if (this->cFileType == 'S') {
this->F_Reads->pQualScores->getQualityScoresFromQUAL(this->F_Reads->pReadsID);
this->R_Reads->pQualScores->getQualityScoresFromQUAL(this->R_Reads->pReadsID);
}
}
/*
unsigned int CPairedReadsSet::get_next_capacity_reads_pairs_from_single_file()
{
bool bStoreQS = (this->R_Reads->pQualScores != NULL) && (this->F_Reads->pQualScores != NULL);
bool bSOLiDReadFormat = (this->cFileType == 'Q' || this->cFileType == 'S');
bool bGetQScores = (this->cFileType == 'Q' || this->cFileType == 'q') && bStoreQS;
this->clearReads();
do {
const char* caNextRead = parser.get_Next_Read(); // get next read and store in this->parser.caNextRead
if (caNextRead[0] == '\0') {
this->parser.pBuf->fflush();
break; // End of the file
} else if (isBadRead(bSOLiDReadFormat, caNextRead, this->longReadLength)) {
this->handleBadread();
} else {
this->save_next_long_read(bSOLiDReadFormat, bGetQScores, this->in5to3cat3to5Format);
}
} while (this->F_Reads->pReadsID->size() < this->F_Reads->pReadsSet->capacity());
printf("Deal read no. %u in %s.\r", this->uiNo_of_Reads, this->InputFile);
this->removeExtraTags();
if(bStoreQS) {
this->getQualityScoresFromQUAL();
}
return((unsigned int)this->R_Reads->pReadsSet->size());
}
*/
unsigned int CPairedReadsSet::getExpReadLength(unsigned int fullReadLength)
{
bool oddReadLength = (fullReadLength % 2 == 1);
unsigned int expFullReadLength = this->uiRead_Length * 2;
if (oddReadLength) {
expFullReadLength --;
}
return(expFullReadLength);
}
void CPairedReadsSet::save_next_read_id(const char* tagLine, char sep)
{
this->F_Reads->save_next_read_id(tagLine, sep);
this->R_Reads->save_next_read_id(tagLine, sep);
}
int CPairedReadsSet::initialization(void)
{
this->uiNo_of_Bad_Reads = 0;
this->uiNo_of_Reads = 0;
this->uiRead_Length = 0;
this->F_Reads = NULL;
this->R_Reads = NULL;
this->pQualScoresF = NULL;
this->pQualScoresR = NULL;
this->in5to3cat3to5Format = false;
return(0);
}
void CPairedReadsSet::handleBadRead(void)
{
// Currently no message for Bad read
if (this->R_Reads->pReadsID->size() > this->R_Reads->uiNo_of_Reads) {
this->R_Reads->pReadsID->pop_back();
}
if (this->F_Reads->pReadsID->size() > this->F_Reads->uiNo_of_Reads) {
this->F_Reads->pReadsID->pop_back();
}
this->uiNo_of_Bad_Reads ++; // double check if the counter is correct
}
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