Method loadBedPEFileIntoMap

src/utils/bedFilePE/bedFilePE.cpp:470–501

void BedFilePE::loadBedPEFileIntoMap() {

    int lineNum = 0;
    int bin1, bin2;
    BedLineStatus bedStatus;
    BEDPE bedpeEntry, nullBedPE;

    Open();
    bedStatus = this->GetNextBedPE(bedpeEntry, lineNum);
    while (bedStatus != BED_INVALID) {

        if (bedStatus == BED_VALID) {
            MATE *bedEntry1 = new MATE();
            MATE *bedEntry2 = new MATE();
            // separate the BEDPE entry into separate
            // BED entries
            splitBedPEIntoBeds(bedpeEntry, lineNum, bedEntry1, bedEntry2);

            // load end1 into a UCSC bin map
            bin1 = getBin(bedEntry1->bed.start, bedEntry1->bed.end);
            this->bedMapEnd1[bedEntry1->bed.chrom][bin1].push_back(*bedEntry1);

            // load end2 into a UCSC bin map
            bin2 = getBin(bedEntry2->bed.start, bedEntry2->bed.end);
            this->bedMapEnd2[bedEntry2->bed.chrom][bin2].push_back(*bedEntry2);

            bedpeEntry = nullBedPE;
        }
        bedStatus = this->GetNextBedPE(bedpeEntry, lineNum);
    }
    Close();
}


void BedFilePE::splitBedPEIntoBeds(const BEDPE &bedpeEntry, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2) {