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;
}
void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *dists) {
const ContextClosest *context = static_cast<const ContextClosest *>(_context);
bool deleteBlocks = false;
RecordKeyVector blockList(keyList.getKey());
if (keyList.getKey()->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()) {
printKey(keyList.getKey());
tab();
addDbFileId((*iter)->getFileIdx());
(*iter)->print(_outBuf);
if (dists != NULL) {
tab();
_outBuf.append((*dists)[distCount]);
distCount++;
}
newline();
if (needsFlush()) flush();
}
} else {
printKey(keyList.getKey());
tab();
null(true, false);
if (context->reportDistance()) {
tab();
_outBuf.append(-1);
}
newline();
}
if (deleteBlocks) {
_bamBlockMgr->deleteBlocks(blockList);
_currBamBlockList = NULL;
}
return;
}
void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx)
{
//get the max start and min end as strings.
const_cast<Record *>(hitRecord)->undoZeroLength();
const QuickString *startStr = NULL;
const QuickString *endStr = NULL;
int maxStart = 0;
int minEnd = 0;
int keyStart = keyRecord->getStartPos();
int keyEnd = keyRecord->getEndPos();
int hitStart = hitRecord->getStartPos();
int hitEnd = hitRecord->getEndPos();
if ( keyStart>= hitStart) {
//the key start is after the hit start, but we need to check and make sure the hit end is at least after the keyStart.
//The reason for this is that, in some rare cases, such as both the key and hit having been zero length intervals,
//the normal process for intersection that allows us to simply report the maxStart and minEnd do not necessarily apply.
if (hitEnd >= keyStart) {
//this is ok. We have a normal intersection where the key comes after the hit.
maxStart = keyStart;
startStr = &(keyRecord->getStartPosStr());
minEnd = min(keyEnd, hitEnd);
endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
} else {
//this is the weird case of not a "real" intersection. The keyStart is greater than the hitEnd. So just report the key as is.
maxStart = keyStart;
minEnd = keyEnd;
startStr = &(keyRecord->getStartPosStr());
endStr = &(keyRecord->getEndPosStr());
}
} else {
//all of the above, but backwards. keyStart is before hitStart.
if (keyEnd >= hitStart) {
//normal intersection, key first
maxStart = hitStart;
startStr = &(hitRecord->getStartPosStr());
minEnd = min(keyEnd, hitEnd);
endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
} else {
//this is the weird case of not a "real" intersection. The hitStart is greater than the keyEnd. So just report the hit as is.
maxStart = hitStart;
minEnd = hitEnd;
startStr = &(hitRecord->getStartPosStr());
endStr = &(hitRecord->getEndPosStr());
}
}
if (!(static_cast<ContextIntersect *>(_context))->getWriteA() && !(static_cast<ContextIntersect *>(_context))->getWriteB()
&& !(static_cast<ContextIntersect *>(_context))->getWriteOverlap() && !(static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
printKey(keyRecord, *startStr, *endStr);
newline();
if (needsFlush()) flush();
}
else if (((static_cast<ContextIntersect *>(_context))->getWriteA() &&
(static_cast<ContextIntersect *>(_context))->getWriteB()) || (static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
printKey(keyRecord);
tab();
addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
newline();
if (needsFlush()) flush();
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteA()) {
printKey(keyRecord);
newline();
if (needsFlush()) flush();
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteB()) {
printKey(keyRecord, *startStr, *endStr);
tab();
addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
newline();
if (needsFlush()) flush();
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteOverlap()) {
int printOverlapBases = 0;
if (_context->getObeySplits()) {
printOverlapBases = _splitInfo->getOverlapBases(hitIdx);
} else {
printOverlapBases = minEnd - maxStart;
}
printKey(keyRecord);
tab();
addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
tab();
int2str(printOverlapBases, _outBuf, true);
newline();
if (needsFlush()) flush();
}
const_cast<Record *>(keyRecord)->adjustZeroLength();
}
void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx)
{
// overlap interval is defined by min(e1,e2) - max(s1,s2)
int maxStart = max(keyRecord->getStartPos(), hitRecord->getStartPos());
int minEnd = min(keyRecord->getEndPos(), hitRecord->getEndPos());
// need to undo our conversion of 1-based start coordinates to 0-based
if (!keyRecord->isZeroBased())
maxStart++;
// all of the different printing scenarios based upon the options used.
if (!(static_cast<ContextIntersect *>(_context))->getWriteA() && !(static_cast<ContextIntersect *>(_context))->getWriteB()
&& !(static_cast<ContextIntersect *>(_context))->getWriteOverlap() && !(static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
const_cast<Record *>(keyRecord)->undoZeroLength();
printKey(keyRecord, maxStart, minEnd);
}
else if (((static_cast<ContextIntersect *>(_context))->getWriteA() &&
(static_cast<ContextIntersect *>(_context))->getWriteB()) || (static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
const_cast<Record *>(keyRecord)->undoZeroLength();
printKey(keyRecord);
tab();
const_cast<Record *>(hitRecord)->undoZeroLength();
addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteA()) {
const_cast<Record *>(keyRecord)->undoZeroLength();
printKey(keyRecord);
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteB()) {
printKey(keyRecord, maxStart, minEnd);
tab();
addDbFileId(hitRecord->getFileIdx());
const_cast<Record *>(hitRecord)->undoZeroLength();
hitRecord->print(_outBuf);
}
else if ((static_cast<ContextIntersect *>(_context))->getWriteOverlap()) {
int printOverlapBases = 0;
if (_context->getObeySplits()) {
printOverlapBases = _context->getSplitBlockInfo()->getOverlapBases(hitIdx);
} else {
// if one of the records was zerolength, the number of
// overlapping bases needs to be corrected
if (keyRecord->isZeroLength() || hitRecord->isZeroLength ())
{
maxStart++;
minEnd--;
}
printOverlapBases = minEnd - maxStart;
}
const_cast<Record *>(keyRecord)->undoZeroLength();
printKey(keyRecord);
tab();
addDbFileId(hitRecord->getFileIdx());
const_cast<Record *>(hitRecord)->undoZeroLength();
hitRecord->print(_outBuf);
tab();
int2str(printOverlapBases, _outBuf, true);
}
newline();
if (needsFlush()) flush();
const_cast<Record *>(hitRecord)->adjustZeroLength();
}
