bool RecordOutputMgr::printKeyAndTerminate(RecordKeyVector &keyList) {
if (_context->getProgram() == ContextBase::MERGE) {
//when printing merged records, we want to force the printing into
//bed3 format, which is surprisingly difficult to do. Had to use the following:
const Bed3Interval *bed3 = static_cast<const Bed3Interval *>(keyList.getKey());
bed3->Bed3Interval::print(_outBuf);
//in addition, if we're doing stranded merges, we need to print the strand sign.
if (_context->getDesiredStrand() != FileRecordMergeMgr::ANY_STRAND) {
_outBuf.append("\t");
_outBuf.append(keyList.getKey()->getStrand());
}
return false;
}
printBamType bamCode = printBamRecord(keyList);
if (bamCode == BAM_AS_BAM) {
return true;
} else if (bamCode == NOT_BAM) {
keyList.getKey()->print(_outBuf);
return false;
}
//otherwise, it was BAM_AS_BED, and the key was printed.
return false;
}
bool RecordOutputMgr::printKeyAndTerminate(RecordKeyVector &keyList) {
if (_context->getProgram() == ContextBase::MERGE) {
//when printing merged records, we want to force the printing into
//bed3 format, which is surprisingly difficult to do. Had to use the following:
const Bed3Interval *bed3 = static_cast<const Bed3Interval *>(keyList.getKey());
bed3->Bed3Interval::print(_outBuf);
return false;
}
printBamType bamCode = printBamRecord(keyList);
if (bamCode == BAM_AS_BAM) {
return true;
} else if (bamCode == NOT_BAM) {
keyList.getKey()->print(_outBuf);
return false;
}
//otherwise, it was BAM_AS_BED, and the key was printed.
return false;
}
void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blockList)
{
if (needsFlush()) {
flush();
}
//The first time we print a record is when we print any header, because the header
//hasn't been read from the query file until after the first record has also been read.
checkForHeader();
const_cast<Record *>(keyList.getKey())->undoZeroLength();
_currBamBlockList = blockList;
if (_context->getProgram() == ContextBase::INTERSECT) {
if (_printable) {
if (keyList.empty()) {
if ((static_cast<ContextIntersect *>(_context))->getWriteAllOverlap()) {
// -wao the user wants to force the reporting of 0 overlap
if (printKeyAndTerminate(keyList)) {
_currBamBlockList = NULL;
return;
}
tab();
null(false, true);
tab();
_outBuf.append('0');
newline();
if (needsFlush()) flush();
}
else if ((static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
if (printKeyAndTerminate(keyList)) {
_currBamBlockList = NULL;
return;
}
tab();
null(false, true);
newline();
if (needsFlush()) flush();
_currBamBlockList = NULL;
return;
}
} else {
if (printBamRecord(keyList, true) == BAM_AS_BAM) {
_currBamBlockList = NULL;
return;
}
int hitIdx = 0;
for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
reportOverlapDetail(keyList.getKey(), *iter, hitIdx);
hitIdx++;
}
}
} else { // not printable
reportOverlapSummary(keyList);
}
_currBamBlockList = NULL;
} else if (_context->getProgram() == ContextBase::SAMPLE) {
if (!printKeyAndTerminate(keyList)) {
newline();
}
_currBamBlockList = NULL;
return;
} else if (_context->getProgram() == ContextBase::MAP) {
printKeyAndTerminate(keyList);
_currBamBlockList = NULL;
return;
} else if (_context->getProgram() == ContextBase::MERGE) {
printKeyAndTerminate(keyList);
_currBamBlockList = NULL;
return;
}
}