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#include "MappingResult.h"
CMappingResult::CMappingResult(void)
{
this->initialization();
}
CMappingResult::CMappingResult(CAlignmentsQ& aQue, unsigned int uiReadLength = 0)
{
initialization();
this->uiReadLength = uiReadLength;
this->uiDiff = aQue.MinDiff; //This is the minimum distance of mappings
this->MultipleMappedNo = aQue.load;
myStrCpy(this->QNAME, aQue.tag, FILENAME_MAX);
// aQue.read.decode(this->caRead);
}
CMappingResult::~CMappingResult(void)
{
;
}
void CMappingResult::initialization(void)
{
this->QNAME[0] = '\0';
this->FLAG = 0;
this->strand = '+';
this->RNAME[0] = '\0';
this->uiPOS = 0;
this->MAPQ = 0;
this->CIGAR[0] = '\0';
this->MRNM[0] = '\0';
this->uiMPOS = 0;
this->ISIZE = 0;
this->caRead[0] = '\0';
this->QScores[0] = '\0';
this->revComRead[0] = '\0';
this->revQScores[0] = '\0';
this->rawScores[0] = '\0';
this->TAG[0] = '\0';
this->SNPtype = ' ';
this->caRef[0] = '\0';
this->mismatchScore = 0;
this->uiReadLength = 0;
this->isColorRead = false;
// this->uiDiff = 0; // TODO uncomment it
}
// currently not used
string get_diff_bases_bt_read_ref(const char* ref, const char* read)
{
char diff_bases_list[MAX_LINE];
vector<int> mis;
for (unsigned int i = 0; read[i] != '\0'; i++) {
if (read[i] != ref[i]) {
mis.push_back(i+1);
}
}
int j = 0;
for (vector<int>::iterator it = mis.begin(); it != mis.end(); it++) {
sprintf(&(diff_bases_list[j]), "%d_%c,", *it, ref[*it]);
j += ((*it < 10) ? 3 : 4); // assume read length < 100
if ( *it >= 100) j++; // assume read length < 1000
}
return(string(diff_bases_list));
}
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