vector<string> CFG::computeFirst(const vector<string>& str)
// for any string of grammar symbols
{
// str = Y1 ...
vector<string> firstStr;
if(str.size() == 1 && str[0] == "")
{
firstStr = {""};
}
else
{
size_t i = 0;
for(; i < str.size(); )
{
vector<string> firstY;
if(str[i] == "$")
{
firstY = {"$"};
}
else
{
firstY = first[getFirstIndex(str[i])].second;
}
bool epsilon = del(firstY, string(""));
add(firstStr, firstY);
if(epsilon)
{
++i;
}
else
{
break;
}
}
if(i == str.size())
{
if(add(firstStr, {""}));
}
}
return firstStr;
}
// When a record is read, check if it is a duplicate or
// store for future checking.
void Dedup_LowMem::checkDups(SamRecord& record, uint32_t recordCount)
{
// Only inside this method if the record is mapped.
// Get the key for this record.
static DupKey key;
key.initKey(record, getLibraryID(record));
int flag = record.getFlag();
bool recordPaired = SamFlag::isPaired(flag) && SamFlag::isMateMapped(flag);
int sumBaseQual = getBaseQuality(record);
int32_t chromID = record.getReferenceID();
int32_t mateChromID = record.getMateReferenceID();
// If we are one-chrom and the mate is not on the same chromosome,
// mark it as not paired.
if(myOneChrom && (chromID != mateChromID))
{
recordPaired = false;
}
// Look in the fragment map to see if an entry for this key exists.
FragmentMapInsertReturn ireturn =
myFragmentMap.insert(std::make_pair(key, FragData()));
FragData* fragData = &(ireturn.first->second);
// Enter the new record in the fragData if (any of the below):
// 1) there is no previous entry for this key (ireturn.second == true)
// or
// 2) the previous entry is not paired
// AND
// a) the new record is paired
// or
// b) the new record has higher quality
if((ireturn.second == true) ||
((fragData->paired == false) &&
(recordPaired || (sumBaseQual > fragData->sumBaseQual))))
{
// Check if this is a new key.
if(ireturn.second == true)
{
// New entry, so build the recalibration table now.
if(myDoRecab)
{
myRecab.processReadBuildTable(record);
}
}
else if(fragData->paired == false)
{
// There was a previous record and it is not paired,
// so mark it as a duplicate.
// Duplicate checking/marking for pairs is handled below.
handleDuplicate(fragData->recordIndex);
}
// Store this record for later duplicate checking.
fragData->sumBaseQual = sumBaseQual;
fragData->recordIndex = recordCount;
fragData->paired = recordPaired;
}
else
{
// Leave the old record in fragData.
// If the new record is not paired, handle it as a duplicate.
if(recordPaired == false)
{
// This record is a duplicate, so mark it and release it.
handleDuplicate(recordCount);
}
}
// Only paired processing is left, so return if not paired.
if(recordPaired == false)
{
// Not paired, no more operations required, so return.
return;
}
// This is a paired record, so check for its mate.
uint64_t readPos =
SamHelper::combineChromPos(chromID,
record.get0BasedPosition());
uint64_t matePos =
SamHelper::combineChromPos(mateChromID,
record.get0BasedMatePosition());
int mateIndex = -1;
MateData* mateData = NULL;
// Check to see if the mate is prior to this record.
if(matePos <= readPos)
{
// The mate map is stored by the mate position, so look for this
// record's position.
// The mate should be in the mate map, so find it.
std::pair<MateMap::iterator,MateMap::iterator> matches =
myMateMap.equal_range(readPos);
// Loop through the elements that matched the pos looking for the mate.
for(MateMap::iterator iter = matches.first;
iter != matches.second; iter++)
{
if(strcmp((*iter).second.readName.c_str(),
record.getReadName()) == 0)
{
// Found the match.
mateData = &((*iter).second);
// Update the quality and track the mate record and index.
sumBaseQual += mateData->sumBaseQual;
mateIndex = mateData->recordIndex;
// Remove the entry from the map.
myMateMap.erase(iter);
break;
}
}
}
if(mateData == NULL)
{
if(matePos >= readPos)
{
// Haven't gotten to the mate yet, so store this record.
MateMap::iterator mateIter =
myMateMap.insert(std::make_pair(matePos, MateData()));
mateIter->second.sumBaseQual = sumBaseQual;
mateIter->second.recordIndex = recordCount;
mateIter->second.key.copy(key);
mateIter->second.readName = record.getReadName();
}
else
{
// Passed the mate, but it was not found.
handleMissingMate(record.getReferenceID(), record.getMateReferenceID());
}
return;
}
// Make the paired key.
PairedKey pkey(key, mateData->key);
// Check to see if this pair is a duplicate.
PairedMapInsertReturn pairedReturn =
myPairedMap.insert(std::make_pair(pkey,PairedData()));
PairedData* storedPair = &(pairedReturn.first->second);
// Get the index for "record 1" - the one with the earlier coordinate.
int record1Index = getFirstIndex(key, recordCount,
mateData->key, mateIndex);
// Check if we have already found a duplicate pair.
// If there is no duplicate found, there is nothing more to do.
if(pairedReturn.second == false)
{
// Duplicate found.
bool keepStored = true;
if(pairedReturn.first->second.sumBaseQual < sumBaseQual)
{
// The new pair has higher quality, so keep that.
keepStored = false;
}
else if(pairedReturn.first->second.sumBaseQual == sumBaseQual)
{
// Same quality, so keep the one with the earlier record1Index.
if(record1Index < storedPair->record1Index)
{
// The new pair has an earlier lower coordinate read,
// so keep that.
keepStored = false;
}
}
// Check to see which one should be kept by checking qualities.
if(keepStored)
{
// The old pair had higher quality so mark the new pair as a
// duplicate and release them.
handleDuplicate(mateIndex);
handleDuplicate(recordCount);
}
else
{
// The new pair has higher quality, so keep that.
// First mark the previous one as duplicates and release them.
handleDuplicate(storedPair->record1Index);
handleDuplicate(storedPair->record2Index);
// Store this pair's information.
if(record1Index == mateIndex)
{
// Mate has a lower coordinate, so make mate
// record1.
storedPair->sumBaseQual = sumBaseQual;
storedPair->record1Index = mateIndex;
storedPair->record2Index = recordCount;
}
else
{
// This record has a lower coordinate, so make it
// record1.
storedPair->sumBaseQual = sumBaseQual;
storedPair->record1Index = recordCount;
storedPair->record2Index = mateIndex;
}
}
}
else
{
// Store this pair's information.
storedPair->sumBaseQual = sumBaseQual;
if(record1Index == mateIndex)
{
// Mate has a lower coordinate, so make mate
// record1.
storedPair->record1Index = mateIndex;
storedPair->record2Index = recordCount;
}
else
{
// This record has a lower coordinate, so make it
// record1.
storedPair->record1Index = recordCount;
storedPair->record2Index = mateIndex;
}
}
}
void CFG::computeFirst()
// elements are terminals
// for all grammar symbols
{
first.clear();
for(size_t i = 0; i < t.size(); ++i)
{
first.push_back(make_pair(t[i], vector<string>({t[i]})));
}
for(size_t i = 0; i < v.size(); ++i)
{
first.push_back(make_pair(v[i], vector<string>()));
}
bool updated = false;
do
{
updated = false;
for(size_t i = 0; i < v.size(); ++i)
{
int xFirstIndex = getFirstIndex(v[i]);
vector<string> firstX = first[xFirstIndex].second;
for(size_t j = 0; j < p.size(); ++j)
{
if(p[j].left == v[i])
// X -> Y1 ...
{
if(p[j].right.size() == 1 && p[j].right[0] == "")
{
if(add(firstX, {""}))
{
updated = true;
}
}
else
{
size_t k = 0;
for(; k < p[j].right.size(); )
{
vector<string> firstY = first[getFirstIndex(p[j].right[k])].second;
del(firstY, string(""));
if(add(firstX, firstY))
{
updated = true;
}
if(in(string(""), firstY))
{
++k;
}
else
{
break;
}
}
if(k == p[j].right.size())
{
if(add(firstX, {""}));
}
}
}
}
first[xFirstIndex].second = firstX;
}
}while(updated);
}
// When a record is read, check if it is a duplicate or
// store for future checking.
void Dedup::checkDups(SamRecord& record, uint32_t recordCount)
{
// Only inside this method if the record is mapped.
// Get the key for this record.
static DupKey key;
static DupKey mateKey;
key.updateKey(record, getLibraryID(record));
int flag = record.getFlag();
bool recordPaired = SamFlag::isPaired(flag) && SamFlag::isMateMapped(flag);
int sumBaseQual = getBaseQuality(record);
int32_t chromID = record.getReferenceID();
int32_t mateChromID = record.getMateReferenceID();
// If we are one-chrom and the mate is not on the same chromosome,
// mark it as not paired.
if(myOneChrom && (chromID != mateChromID))
{
recordPaired = false;
}
// Look in the map to see if an entry for this key exists.
FragmentMapInsertReturn ireturn =
myFragmentMap.insert(std::make_pair(key, ReadData()));
ReadData* readData = &(ireturn.first->second);
// Mark this record's data in the fragment record if this is the first
// entry or if it is a duplicate and the old record is not paired and
// the new record is paired or the has a higher quality.
if((ireturn.second == true) ||
((readData->paired == false) &&
(recordPaired || (sumBaseQual > readData->sumBaseQual))))
{
// If there was a previous record, mark it duplicate and release
// the old record
if(ireturn.second == false)
{
// Mark the old record as a DUPLICATE!
handleDuplicate(readData->recordIndex, readData->recordPtr);
}
// Store this record for later duplicate checking.
readData->sumBaseQual = sumBaseQual;
readData->recordIndex = recordCount;
readData->paired = recordPaired;
if(recordPaired)
{
readData->recordPtr = NULL;
}
else
{
readData->recordPtr = &record;
}
}
else
{
// The old record is not a duplicate so the new record is
// a duplicate if it is not paired.
if(recordPaired == false)
{
// This record is a duplicate, so mark it and release it.
handleDuplicate(recordCount, &record);
}
}
// Only paired processing is left, so return if not paired.
if(recordPaired == false)
{
// Not paired, no more operations required, so return.
return;
}
// This is a paired record, so check for its mate.
uint64_t readPos =
SamHelper::combineChromPos(chromID,
record.get0BasedPosition());
uint64_t matePos =
SamHelper::combineChromPos(mateChromID,
record.get0BasedMatePosition());
SamRecord* mateRecord = NULL;
int mateIndex = 0;
// Check to see if the mate is prior to this record.
if(matePos <= readPos)
{
// The mate map is stored by the mate position, so look for this
// record's position.
// The mate should be in the mate map, so find it.
std::pair<MateMap::iterator,MateMap::iterator> matches =
myMateMap.equal_range(readPos);
// Loop through the elements that matched the pos looking for the mate.
for(MateMap::iterator iter = matches.first;
iter != matches.second; iter++)
{
if(strcmp((*iter).second.recordPtr->getReadName(),
record.getReadName()) == 0)
{
// Found the match.
ReadData* mateData = &((*iter).second);
// Update the quality and track the mate record and index.
sumBaseQual += mateData->sumBaseQual;
mateIndex = mateData->recordIndex;
mateRecord = mateData->recordPtr;
// Remove the entry from the map.
myMateMap.erase(iter);
break;
}
}
}
if((mateRecord == NULL) && (matePos >= readPos))
{
// Haven't gotten to the mate yet, so store this record.
MateMap::iterator mateIter =
myMateMap.insert(std::make_pair(matePos, ReadData()));
mateIter->second.sumBaseQual = sumBaseQual;
mateIter->second.recordPtr = &record;
mateIter->second.recordIndex = recordCount;
// No more processing for this record is necessary.
return;
}
if(mateRecord == NULL)
{
// Passed the mate, but it was not found.
handleMissingMate(&record);
return;
}
// Make the paired key.
mateKey.updateKey(*mateRecord, getLibraryID(*mateRecord));
PairedKey pkey(key, mateKey);
// Check to see if this pair is a duplicate.
PairedMapInsertReturn pairedReturn =
myPairedMap.insert(std::make_pair(pkey,PairedData()));
PairedData* storedPair = &(pairedReturn.first->second);
// Get the index for "record 1" - the one with the earlier coordinate.
int record1Index = getFirstIndex(key, recordCount,
mateKey, mateIndex);
// Check if we have already found a duplicate pair.
// If there is no duplicate found, there is nothing more to do.
if(pairedReturn.second == false)
{
// Duplicate found.
bool keepStored = true;
if(pairedReturn.first->second.sumBaseQual < sumBaseQual)
{
// The new pair has higher quality, so keep that.
keepStored = false;
}
else if(pairedReturn.first->second.sumBaseQual == sumBaseQual)
{
// Same quality, so keep the one with the earlier record1Index.
if(record1Index < storedPair->record1Index)
{
// The new pair has an earlier lower coordinate read,
// so keep that.
keepStored = false;
}
}
// Check to see which one should be kept by checking qualities.
if(keepStored)
{
// The old pair had higher quality so mark the new pair as a
// duplicate and release them.
handleDuplicate(mateIndex, mateRecord);
handleDuplicate(recordCount, &record);
}
else
{
// The new pair has higher quality, so keep that.
// First mark the previous one as duplicates and release them.
handleDuplicate(storedPair->record1Index, storedPair->record1Ptr);
handleDuplicate(storedPair->record2Index, storedPair->record2Ptr);
// Store this pair's information.
if(record1Index == mateIndex)
{
// Mate has a lower coordinate, so make mate
// record1.
storedPair->sumBaseQual = sumBaseQual;
storedPair->record1Ptr = mateRecord;
storedPair->record2Ptr = &record;
storedPair->record1Index = mateIndex;
storedPair->record2Index = recordCount;
}
else
{
// This record has a lower coordinate, so make it
// record1.
storedPair->sumBaseQual = sumBaseQual;
storedPair->record1Ptr = &record;
storedPair->record2Ptr = mateRecord;
storedPair->record1Index = recordCount;
storedPair->record2Index = mateIndex;
}
}
}
else
{
// Store this pair's information.
storedPair->sumBaseQual = sumBaseQual;
if(record1Index == mateIndex)
{
// Mate has a lower coordinate, so make mate
// record1.
storedPair->record1Ptr = mateRecord;
storedPair->record2Ptr = &record;
storedPair->record1Index = mateIndex;
storedPair->record2Index = recordCount;
}
else
{
// This record has a lower coordinate, so make it
// record1.
storedPair->record1Ptr = &record;
storedPair->record2Ptr = mateRecord;
storedPair->record1Index = recordCount;
storedPair->record2Index = mateIndex;
}
}
}
