void RecordOutputMgr::printRecord(const Record *record, const QuickString & value)
{
_afterVal = value;
printRecord(record);
if (!value.empty()) {
tab();
_outBuf.append(value);
}
newline();
if (needsFlush()) flush();
}
bool ComplementFile::fastForward(const QuickString &newChrom) {
if (!newChrom.empty() && !_genomeFile->hasChrom(newChrom)) return false;
int i= _currPosInGenomeList +1;
while (i < (int)_chromList.size() && _chromList[i] != newChrom) {
_outRecord.setChrName(_chromList[i]);
_currStartPos = 0;
int endPos = _genomeFile->getChromSize(_chromList[i]);
printRecord(endPos);
i++;
}
if (newChrom.empty()) return true;
if (i== (int)_chromList.size()) {
//reached end but didn't find new chrom. Genome and DB are not sorted in same order.
cerr << "***** ERROR: genome file and input file are not sorted in same order. Exiting..." << endl;
exit(1);
//this is where we'd return false if we weren't exiting.
}
_currChrom = newChrom;
_currPosInGenomeList = i;
return true;
}
void RecordOutputMgr::printRecord(const Record *record, const QuickString & value)
{
_afterVal = value;
bool recordPrinted = false;
if (record != NULL) {
printRecord(record);
recordPrinted = true;
}
if (!value.empty()) {
if (recordPrinted) tab();
_outBuf.append(value);
}
newline();
if (needsFlush()) flush();
}