void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *dists) {
//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 ContextClosest *context = static_cast<const ContextClosest *>(_context);
bool deleteBlocks = false;
const Record *keyRec = keyList.getKey();
RecordKeyVector blockList(keyRec);
if (keyRec->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
_bamBlockMgr->getBlocks(blockList, deleteBlocks);
_currBamBlockList = &blockList;
}
if (!keyList.empty()) {
int distCount = 0;
for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
const Record *hitRec = *iter;
printKey(keyRec, keyRec->getStartPosStr(), keyRec->getEndPosStr());
tab();
addDbFileId(hitRec->getFileIdx());
printKey(hitRec, hitRec->getStartPosStr(), hitRec->getEndPosStr());
if (dists != NULL) {
tab();
int dist = (*dists)[distCount];
//if not using sign distance, use absolute value instead.
dist = context->signDistance() ? dist : abs(dist);
_outBuf.append(dist);
distCount++;
}
newline();
if (needsFlush()) flush();
}
} else {
printKey(keyRec, keyRec->getStartPosStr(), keyRec->getEndPosStr());
tab();
// need to add a dummy file id if multiple DB files are used
if (_context->getNumInputFiles() > 2) {
_outBuf.append('.');
tab();
}
null(false, true);
if (context->reportDistance()) {
tab();
_outBuf.append(-1);
}
newline();
}
if (deleteBlocks) {
_bamBlockMgr->deleteBlocks(blockList);
_currBamBlockList = NULL;
}
return;
}
RecordOutputMgr::~RecordOutputMgr()
{
// In the rare case when a file had a header but was otherwise empty,
// we'll need to make a last check to see if the header still needs to be printed.
checkForHeader();
if (_outBuf.size() > 0) {
flush();
}
if (_bamWriter != NULL) {
_bamWriter->Close();
delete _bamWriter;
_bamWriter = NULL;
}
delete _bamBlockMgr;
_bamBlockMgr = NULL;
}
void RecordOutputMgr::printRecord(const Record *record, const QuickString & value)
{
checkForHeader();
_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();
}
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;
}
}
