void ComplementFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
{
_outputMgr = outputMgr;
const Record *rec = hits.getKey();
//test for chrom change.
const QuickString &newChrom = rec->getChrName();
if (_currChrom != newChrom) {
outPutLastRecordInPrevChrom();
//if record's chrom doesn't exist in the genome file, do
//nothing
if (!fastForward(newChrom)) return;
//we've switched to a new chromosome that is in both the DB
//and genome file.
_currStartPos = 0;
_currChrom = newChrom;
_outRecord.setChrName(newChrom);
}
int endPos = rec->getStartPos();
printRecord(endPos);
_currStartPos = rec->getEndPos();
}
void ComplementFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
{
_outputMgr = outputMgr;
const Record *rec = hits.getKey();
//test for chrom change.
const string &newChrom = rec->getChrName();
if (_currChrom != newChrom) {
outPutLastRecordInPrevChrom();
//if record's chrom doesn't exist in the genome file, do
//nothing
if (!fastForward(newChrom)) return;
//we've switched to a new chromosome that is in both the DB
//and genome file.
_currStartPos = 0;
_currChrom = newChrom;
_outRecord.setChrName(newChrom);
}
// warn if the record's interval is beyond the
// length of the chromosome
checkCoordinatesAgainstChromLength(rec);
// safe guard against the first record for the chrom
// starting with 0.
if (rec->getStartPos() != 0)
{
CHRPOS endPos = rec->getStartPos();
printRecord(endPos);
}
_currStartPos = rec->getEndPos();
}
bool ComplementFile::finalizeCalculations() {
outPutLastRecordInPrevChrom();
fastForward("");
return true;
}
void ComplementFile::giveFinalReport(RecordOutputMgr *outputMgr) {
_outputMgr = outputMgr;
outPutLastRecordInPrevChrom();
fastForward("");
}
