/usr/include/pbseq/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp is in libblasr-dev 0~20161219-2.
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The actual contents of the file can be viewed below.
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#define _BLASR_FIND_MAX_INTERVAL_IMPL_HPP_
template<typename T_Sequence, typename T_AnchorList>
float DefaultWeightFunction<T_Sequence, T_AnchorList>::operator() (
T_Sequence &text, T_Sequence &read, T_AnchorList matchPosList) {
PB_UNUSED(text);
PB_UNUSED(read);
int i;
float weight = 0;
for (i = 0; i < matchPosList.size(); i++) {
weight += matchPosList[i].weight();
}
return weight;
}
template<typename T_Pos>
int MatchPosQueryOrderFunctor<T_Pos>::operator()(T_Pos &pos) {
return pos.q;
}
template<typename T_MatchList>
void PrintLIS(T_MatchList &matchList, DNALength curPos,
DNALength curGenomePos, DNALength nextGenomePos,
DNALength clp, DNALength cle) {
int i;
cout << curPos << " " << curGenomePos << " "
<< nextGenomePos << " " << clp << " " << cle << endl;
for (i = 0; i < matchList.size(); i++) {
cout.width(8);
cout << matchList[i].l << " ";
}
cout << endl;
for (i = 0; i < matchList.size(); i++) {
cout.width(8);
cout << matchList[i].q << " ";
}
cout << endl;
for (i = 0; i < matchList.size(); i++) {
cout.width(8);
cout << matchList[i].t << " ";
}
cout << endl << endl;
}
template<typename T_MatchList, typename T_SequenceDB>
void FilterMatchesAsLIMSTemplateSquare(T_MatchList &matches,
DNALength queryLength, DNALength limsTemplateLength,
T_SequenceDB &seqDB) {
int seqIndex;
//
// Make sure there is sequence coordinate information.
//
if (seqDB.nSeqPos == 0) {
return;
}
int matchIndex = 0;
for (seqIndex = 1; seqIndex < seqDB.nSeqPos; seqIndex++) {
DNALength refLength = seqDB.seqStartPos[seqIndex] -
seqDB.seqStartPos[seqIndex - 1];
// account for indel error.
refLength = queryLength * 1.15 + limsTemplateLength;
//
// Flag matches that are beyond the (rough) square with the length
// of the query for removal.
//
while (matchIndex < matches.size() and
matches[matchIndex].t < seqDB.seqStartPos[seqIndex]) {
if (matches[matchIndex].t > seqDB.seqStartPos[seqIndex-1]
+ refLength) {
matches[matchIndex].l = 0;
}
matchIndex++;
}
int curMatchIndex = 0;
matchIndex = 0;
for (matchIndex = 0; matchIndex < matches.size(); matchIndex++) {
if (matches[matchIndex].l != 0) {
matches[curMatchIndex] = matches[matchIndex];
curMatchIndex++;
}
}
matches.resize(curMatchIndex);
}
}
template<typename T_MatchList, typename T_SequenceBoundaryDB>
void AdvanceIndexToPastInterval(T_MatchList &pos, DNALength nPos,
DNALength intervalLength, DNALength contigLength,
T_SequenceBoundaryDB &SeqBoundary,
DNALength startIndex, DNALength startIntervalBoundary,
DNALength &index, DNALength &indexIntervalBoundary) {
(void)(contigLength);
if (index >= pos.size()) {
return;
}
indexIntervalBoundary = SeqBoundary(pos[index].t);
DNALength boundaryIndex = SeqBoundary.GetIndex(pos[index].t);
DNALength nextBoundary = SeqBoundary.GetStartPos(boundaryIndex + 1);
(void)(nextBoundary);
while (// index is not past the end of the genome
index < nPos and
//
// Stop when the index goes too far ahead.
//
pos[index].t - pos[startIndex].t <= intervalLength and
//
// Still searching in the current contig.
//
indexIntervalBoundary == startIntervalBoundary) {
index++;
if (index < nPos) {
indexIntervalBoundary = SeqBoundary(pos[index].t);
}
}
}
template<typename T_MatchList>
int RemoveZeroLengthAnchors(T_MatchList &matchList) {
int origSize = matchList.size();
int cur = 0;
for (size_t m = 0; m < matchList.size(); m++) {
if (matchList[m].l > 0) {
matchList[cur] = matchList[m];
cur++;
}
}
matchList.resize(cur);
return origSize - cur;
}
template<typename T_MatchList>
int RemoveOverlappingAnchors(T_MatchList &matchList) {
int m;
int n;
for (m = int(matchList.size()); m > 0; m--) {
n = m - 1;
//
// Skip past repeats in the query.
while (n > 0 and matchList[n].t == matchList[m].t) {
n--;
}
bool mergeFound = false;
int ni = n;
while (mergeFound == false and
n > 0 and
matchList[n].t == matchList[ni].t) {
if (matchList[n].q < matchList[m].q and
matchList[n].t < matchList[m].t and
matchList[n].l + matchList[n].q >=
matchList[m].l + matchList[m].q and
matchList[n].l + matchList[n].t >=
matchList[m].l + matchList[m].t) {
matchList[m].l = 0;
mergeFound = true;
}
n--;
}
}
int numRemoved = RemoveZeroLengthAnchors(matchList);
return numRemoved;
}
template<typename T_MatchList>
int SumAnchors(T_MatchList &pos, int start, int end) {
int sum = 0;
int i;
for (i = start; i < end; i++) {
sum += pos[i].l;
}
return sum;
}
template<typename T_MatchList,
typename T_SequenceBoundaryDB>
void StoreLargestIntervals(
T_MatchList &pos,
// End search for intervals at boundary positions
// stored in seqBoundaries
T_SequenceBoundaryDB & ContigStartPos,
// parameters
// How many values to search through for a max set.
DNALength intervalLength,
// How many sets to keep track of
int minSize,
vector<DNALength> &start,
vector<DNALength> &end) {
if (pos.size() == 0) {
return;
}
//
// Search for clusters of intervals within the pos array within
// pos[cur...next). The value of 'next' should be the first anchor
// outside the possible range to cluster, or the end of the anchor list.
VectorIndex cur = 0;
VectorIndex nPos = pos.size();
VectorIndex next = cur + 1;
DNALength curBoundary = 0, nextBoundary = 0;
DNALength contigLength = ContigStartPos.Length(pos[cur].t);
DNALength endOfCurrentInterval = curBoundary + contigLength;
PB_UNUSED(curBoundary);
PB_UNUSED(nextBoundary);
PB_UNUSED(endOfCurrentInterval);
curBoundary = ContigStartPos(pos[cur].t);
nextBoundary = ContigStartPos(pos[next].t);
//
// Advance next until the anchor is outside the interval that
// statrts at 'cur', and is inside the same contig that the anchor
// at cur is in.
//
DNALength curIntervalLength = NumRemainingBases(pos[cur].q, intervalLength);
PB_UNUSED(curIntervalLength);
AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
cur, curBoundary, next, nextBoundary);
DNALength maxStart = cur, maxEnd = next;
int maxSize = SumAnchors(pos, cur, next);
int curSize = maxSize;
if (curSize > minSize) {
start.push_back(cur);
end.push_back(next);
}
while ( cur < nPos ) {
//
// This interval overlaps with a possible max start
//
if (pos[cur].t >= pos[maxStart].t and maxEnd > 0 and pos[cur].t < pos[maxEnd-1].t) {
if (curSize > maxSize) {
maxSize = curSize;
maxStart = cur;
maxEnd = next;
}
}
else {
if (maxSize > minSize) {
start.push_back(maxStart);
end.push_back(maxEnd);
}
maxStart = cur;
maxEnd = next;
maxSize = curSize;
}
//
// Done scoring current interval. At this point the range
// pos[cur...next) has been searched for a max increasing
// interval. Find a new range that will possibly yield a new
// maximum interval.
// There are a few cases to consider:
//
//
// genome |---+----+------------+------+-----------------------|
// anchors cur cur+1 next next+1
//
// Case 1. The range on the target pos[ cur+1 ... next].t is a
// valid interval (it is roughly the length of the read). In this
// case increase cur and next by 1, and search this range.
//
// genome |---+----+------------+------+-----------------------|
// cur cur+1 next next+1
// read interval ====================
//
// Case 2. The range on the target pos[cur+1 ... next] is not a
// valid interval, and it is much longer than the length of the
// read. This implies that it is impossible to increase the score
// of the read by including both
//
// genome |---+----+--------------------------------+-----+---|
// cur cur+1 next next+1
// read interval ====================
//
// Advance the interval until it includes the next anchor
//
// genome |---+----+------------------+-------------+-----+---|
// cur cur+1 cur+n next next+1
// read interval ====================
//
// First advance pointer in anchor list. If this advances to the
// end, done and no need for further logic checking (break now).
//
// If the next position is not within the same contig as the current,
// advance the current to the next since it is impossible to find
// any more intervals in the current pos.
//
bool recountInterval = false;
if (curBoundary != nextBoundary) {
cur = next;
curBoundary = nextBoundary;
//
// Start the search for the first interval in the next contig
// just after the current position.
//
if (next < nPos) {
next = cur + 1;
}
}
else {
//
// The next interval is in the same contig as the current interval.
// Make sure not to double count the current interval.
//
curSize -= pos[cur].l;
cur++;
if (cur >= nPos)
break;
//
// Advance the next to outside this interval.
//
curSize += pos[next].l;
if (pos[next].t - pos[cur].t > intervalLength) {
if (maxSize > minSize) {
start.push_back(maxStart);
end.push_back(maxEnd);
}
cur = next;
recountInterval = true;
maxSize = 0;
}
next++;
}
if (next > nPos) {
//
// Searched last interval, done.
//
break;
}
//
// Next has advanced. Check what contig it is in.
//
if (next < nPos) {
nextBoundary = ContigStartPos(pos[next].t);
//
// Advance next to the maximum position within this contig that is
// just after where the interval starting at cur is, or the first
// position in the next contig.
//
VectorIndex prevNext = next;
AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
cur, curBoundary, next, nextBoundary);
if (prevNext != next or recountInterval) {
curSize = SumAnchors(pos, cur, next);
}
}
// if next >= nPos, the boundary stays the same.
//
// When searching multiple contigs, it is important to know the
// boundary of the contig that this anchor is in so that clusters
// do not span multiple contigs. Find the (right hand side)
// boundary of the current contig.
//
curBoundary = ContigStartPos(pos[cur].t);
contigLength = ContigStartPos.Length(pos[cur].t);
//
// Previously tried to advance half. This is being removed since
// proper heuristics are making it not necessary to use.
//
}
if (curSize > minSize) {
start.push_back(maxStart);
end.push_back(maxEnd);
}
}
template<typename T_MatchList,
typename T_PValueFunction,
typename T_WeightFunction,
typename T_SequenceBoundaryDB,
typename T_ReferenceSequence,
typename T_Sequence>
int FindMaxIncreasingInterval(
// Input
// readDir is used to indicate if the interval that is being stored is
// in the forward or reverse strand. This is important later when
// refining alignments so that the correct sequence is aligned back
// to the reference.
int readDir,
T_MatchList &pos,
// How many values to search through for a max set.
DNALength intervalLength,
// How many sets to keep track of
VectorIndex nBest,
// End search for intervals at boundary positions
// stored in seqBoundaries
T_SequenceBoundaryDB & ContigStartPos,
// First rand intervals by their p-value
T_PValueFunction &MatchPValueFunction,
// When ranking intervals, sum over weights determined by
// MatchWeightFunction
T_WeightFunction &MatchWeightFunction,
// Output.
// The increasing interval coordinates,
// in order by queue weight.
WeightedIntervalSet &intervalQueue,
T_ReferenceSequence &reference,
T_Sequence &query,
IntervalSearchParameters ¶ms,
vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
ClusterList &clusterList,
VarianceAccumulator<float> &accumPValue,
VarianceAccumulator<float> &accumWeight,
VarianceAccumulator<float> &accumNumAnchorBases) {
(void)(accumNumAnchorBases);
int maxLISSize = 0;
if (params.fastMaxInterval) {
maxLISSize = FastFindMaxIncreasingInterval(
readDir, pos, intervalLength,
nBest, ContigStartPos,
MatchPValueFunction, MatchWeightFunction,
intervalQueue, reference, query,
params, chainEndpointBuffer, clusterList,
accumPValue, accumWeight);
} else {
maxLISSize = ExhaustiveFindMaxIncreasingInterval(
readDir, pos, intervalLength,
nBest, ContigStartPos,
MatchPValueFunction, MatchWeightFunction,
intervalQueue, reference, query,
params, chainEndpointBuffer, clusterList,
accumPValue, accumWeight);
}
if (params.aggressiveIntervalCut and intervalQueue.size() >= 3) {
// aggressiveIntervalCut mode:
// only pick up the most promising intervals if we can classify
// intervals into 'promising' and 'non-promising' clusters.
WeightedIntervalSet::iterator it = intervalQueue.begin();
int sz = intervalQueue.size();
vector<float> pValues, ddPValues;
pValues.resize(sz);
ddPValues.resize(sz);
float sumPValue = 0;
int i = 0;
for(; it != intervalQueue.end(); i++,it++) {
sumPValue += (*it).pValue;
pValues[i] = (*it).pValue;
}
//We will attemp to divide intervals into two clusters, promising
//and non-promising.
float prevSumPValue = pValues[0];
// ddPValue[i], where i in [1...n-2] is the difference of
// (1) (mean pvalue of [0...i-1] minus pvalue[i])
// and
// (2) (pvalue[i] minus mean pvalue of [i+1...n-1])
// pValues are all negative, the lower the better.
// if ddPValue is negative, interval i is closer to cluster [i+1...n-1],
// otherwise, interval i is closer to cluster [0..i-1].
it = intervalQueue.begin();
it ++; //both it and i should point to the second interval in intervalQueue.
for(i = 1; i < sz - 1; i++,it++) {
ddPValues[i] = (prevSumPValue / i) +
(sumPValue - prevSumPValue - pValues[i]) / (sz - i - 1) -
2 * pValues[i];
if (ddPValues[i] <= params.ddPValueThreshold) {
// PValue of interval i is much closer to cluster [i+1...n-1] than
// to cluster [0...i-1]. Mean pValue of cluster [0..i-1]
// minus mean pvalue of cluster [i+1...n-1] < 2 * -500
break;
}
prevSumPValue += pValues[i];
}
if (it != intervalQueue.end()) {
// Erase intervals in the non-promising cluster.
intervalQueue.erase(it, intervalQueue.end());
// Recompute accumPValue, accmWeight, clusterList;
accumPValue.Reset();
accumWeight.Reset();
clusterList.Clear();
for(it = intervalQueue.begin(); it != intervalQueue.end(); it++) {
accumPValue.Append((*it).pValue);
accumWeight.Append((*it).size);
clusterList.Store((*it).totalAnchorSize, (*it).start, (*it).end, (*it).nAnchors);
}
}
}
return maxLISSize;
}
template<typename T_MatchList,
typename T_PValueFunction,
typename T_WeightFunction,
typename T_SequenceBoundaryDB,
typename T_ReferenceSequence,
typename T_Sequence>
int FastFindMaxIncreasingInterval(
// Input
// readDir is used to indicate if the interval that is being stored is in the forward
// or reverse strand. This is important later when refining alignments so that the
// correct sequene is aligned back to the reference.
int readDir,
T_MatchList &pos,
// How many values to search through for a max set.
DNALength intervalLength,
// How many sets to keep track of
VectorIndex nBest,
// End search for intervals at boundary positions
// stored in seqBoundaries
T_SequenceBoundaryDB & ContigStartPos,
// First rand intervals by their p-value
T_PValueFunction &MatchPValueFunction,
// When ranking intervals, sum over weights determined by MatchWeightFunction
T_WeightFunction &MatchWeightFunction,
// Output.
// The increasing interval coordinates,
// in order by queue weight.
WeightedIntervalSet &intervalQueue,
T_ReferenceSequence &reference,
T_Sequence &query,
IntervalSearchParameters ¶ms,
vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
ClusterList &clusterList,
VarianceAccumulator<float> &accumPValue,
VarianceAccumulator<float> &accumWeight) {
(void)(nBest); (void)(query); (void)(reference);
WeightedIntervalSet sdpiq;
VectorIndex cur = 0;
vector<VectorIndex> lisIndices;
//
// Initialize the first interval.
//
if (pos.size() == 0) {
return 0;
}
int lisSize;
float lisPValue;
T_MatchList lis;
int noOvpLisSize = 0;
int noOvpLisNBases = 0;
//
// Search for clusters of intervals within the pos array within
// pos[cur...next). The value of 'next' should be the first anchor
// outside the possible range to cluster, or the end of the anchor list.
VectorIndex next = cur + 1;
DNALength curBoundary = 0, nextBoundary = 0;
DNALength contigLength = ContigStartPos.Length(pos[cur].t);
DNALength endOfCurrentInterval = curBoundary + contigLength;
(void)(curBoundary); (void)(nextBoundary); (void)(endOfCurrentInterval);
vector<UInt> scores, prevOpt;
vector<DNALength> start, end;
StoreLargestIntervals(pos, ContigStartPos, intervalLength, 30, start, end);
VectorIndex i;
VectorIndex posi;
int maxLISSize = 0;
for (posi = 0; posi < start.size(); posi++) {
lis.clear();
lisIndices.clear();
cur = start[posi];
next = end[posi];
if (next - cur == 1) {
//
// Just one match in this interval, don't invoke call to global chain since it is given.
//
lisSize = 0;
lisIndices.push_back(0);
}
else {
//
// Find the largest set of increasing intervals that do not overlap.
//
if (params.globalChainType == 0) {
lisSize = GlobalChain<ChainedMatchPos, BasicEndpoint<ChainedMatchPos> >(pos, cur, next,
lisIndices, chainEndpointBuffer);
}
else {
//
// A different call that allows for indel penalties.
//
lisSize = RestrictedGlobalChain(&pos[cur],next - cur, 0.1, lisIndices, scores, prevOpt);
}
}
// Maybe this should become a function?
for (i = 0; i < lisIndices.size(); i++) {
lis.push_back(pos[lisIndices[i]+cur]);
}
//
// Compute pvalue of this match.
//
if (lis.size() > 0) {
lisPValue = MatchPValueFunction.ComputePValue(lis, noOvpLisNBases, noOvpLisSize);
}
else {
lisPValue = 0;
}
if (lisSize > maxLISSize) {
maxLISSize = lisSize;
}
//
// Insert the interval into the interval queue maintaining only the
// top 'nBest' intervals.
//
//WeightedIntervalSet::iterator lastIt = intervalQueue.begin();
MatchWeight lisWeight = MatchWeightFunction(lis);
VectorIndex lisEnd = lis.size() - 1;
accumPValue.Append(lisPValue);
accumWeight.Append(lisWeight);
if (lisPValue < params.maxPValue and lisSize > 0) {
WeightedInterval weightedInterval(lisWeight, noOvpLisSize, noOvpLisNBases,
lis[0].t, lis[lisEnd].t + lis[lisEnd].GetLength(),
readDir, lisPValue,
lis[0].q, lis[lisEnd].q + lis[lisEnd].GetLength(),
lis);
intervalQueue.insert(weightedInterval);
if (weightedInterval.isOverlapping == false) {
clusterList.Store((float)noOvpLisNBases, lis[0].t, lis[lis.size()-1].t, noOvpLisSize);
}
if (params.verbosity > 1) {
cout << "Weighted Interval to insert:"<< endl << weightedInterval << endl;
cout << "Interval Queue:"<< endl << intervalQueue << endl;
}
}
}
return maxLISSize;
}
template<typename T_MatchList,
typename T_PValueFunction,
typename T_WeightFunction,
typename T_SequenceBoundaryDB,
typename T_ReferenceSequence,
typename T_Sequence>
int ExhaustiveFindMaxIncreasingInterval(
// Input
// readDir is used to indicate if the interval that is being stored is in the forward
// or reverse strand. This is important later when refining alignments so that the
// correct sequene is aligned back to the reference.
int readDir,
T_MatchList &pos,
// How many values to search through for a max set.
DNALength intervalLength,
// How many sets to keep track of
VectorIndex nBest,
// End search for intervals at boundary positions
// stored in seqBoundaries
T_SequenceBoundaryDB & ContigStartPos,
// First rand intervals by their p-value
T_PValueFunction &MatchPValueFunction,
// When ranking intervals, sum over weights determined by MatchWeightFunction
T_WeightFunction &MatchWeightFunction,
// Output.
// The increasing interval coordinates,
// in order by queue weight.
WeightedIntervalSet &intervalQueue,
T_ReferenceSequence &reference,
T_Sequence &query,
IntervalSearchParameters ¶ms,
vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
ClusterList &clusterList,
VarianceAccumulator<float> &accumPValue,
VarianceAccumulator<float> &accumWeight) {
(void)(nBest); (void)(query); (void)(reference);
WeightedIntervalSet sdpiq;
VectorIndex cur = 0;
VectorIndex nPos = pos.size();
//
// Initialize the first interval.
//
if (pos.size() == 0) {
return 0;
}
int lisSize;
float lisPValue;
T_MatchList lis;
int noOvpLisSize = 0;
int noOvpLisNBases = 0;
//
// Search for clusters of intervals within the pos array within
// pos[cur...next). The value of 'next' should be the first anchor
// outside the possible range to cluster, or the end of the anchor list.
VectorIndex next = cur + 1;
DNALength curBoundary = 0, nextBoundary = 0;
DNALength contigLength = ContigStartPos.Length(pos[cur].t);
DNALength endOfCurrentInterval = curBoundary + contigLength;
(void)(curBoundary); (void)(nextBoundary); (void)(endOfCurrentInterval);
curBoundary = ContigStartPos(pos[cur].t);
nextBoundary = ContigStartPos(pos[next].t);
vector<UInt> scores, prevOpt;
//
// Advance next until the anchor is outside the interval that
// statrts at 'cur', and is inside the same contig that the anchor
// at cur is in.
//
DNALength curIntervalLength = NumRemainingBases(pos[cur].q, intervalLength);
(void)(curIntervalLength);
AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
cur, curBoundary, next, nextBoundary);
vector<VectorIndex> lisIndices;
VectorIndex i;
//
// Do some preprocessing. If the number of anchors considered for this hit is 1,
// the global chain is this sole ancor. Don't bother calling GlobalChain
// since it allocates and deallocates extra memory.
//
int maxLISSize = 0;
//
// Search intervals until cur reaches the end of the list of
// anchors.
//
while ( cur < nPos ) {
//
// Search the local interval for a LIS larger than a previous LIS.
//
lis.clear();
lisIndices.clear();
if (next - cur == 1) {
//
// Just one match in this interval, don't invoke call to global chain since it is given.
//
lisSize = 1;
lisIndices.push_back(0);
}
else {
//
// Find the largest set of increasing intervals that do not overlap.
//
if (params.globalChainType == 0) {
lisSize = GlobalChain<ChainedMatchPos, BasicEndpoint<ChainedMatchPos> >(pos, cur, next,
lisIndices, chainEndpointBuffer);
}
else {
//
// A different call that allows for indel penalties.
//
lisSize = RestrictedGlobalChain(&pos[cur],next - cur, 0.1, lisIndices, scores, prevOpt);
}
}
// Maybe this should become a function?
for (i = 0; i < lisIndices.size(); i++) { lis.push_back(pos[lisIndices[i]+cur]); }
//
// Compute pvalue of this match.
//
lisPValue = MatchPValueFunction.ComputePValue(lis, noOvpLisNBases, noOvpLisSize);
if (lisSize > maxLISSize) {
maxLISSize = lisSize;
}
//
// Insert the interval into the interval queue maintaining only the
// top 'nBest' intervals.
//
//WeightedIntervalSet::iterator lastIt = intervalQueue.begin();
MatchWeight lisWeight = MatchWeightFunction(lis);
VectorIndex lisEnd = lis.size() - 1;
accumPValue.Append(lisPValue);
accumWeight.Append(lisWeight);
if (lisPValue < params.maxPValue and lisSize > 0) {
WeightedInterval weightedInterval(lisWeight, noOvpLisSize, noOvpLisNBases,
lis[0].t, lis[lisEnd].t + lis[lisEnd].GetLength(),
readDir, lisPValue,
lis[0].q, lis[lisEnd].q + lis[lisEnd].GetLength(),
lis);
intervalQueue.insert(weightedInterval);
if (weightedInterval.isOverlapping == false) {
clusterList.Store((float)noOvpLisNBases, lis[0].t, lis[lis.size()-1].t, noOvpLisSize);
}
if (params.verbosity > 1) {
cout << "Weighted Interval to insert:"<< endl << weightedInterval << endl;
cout << "Interval Queue:"<< endl << intervalQueue << endl;
}
}
//
// Done scoring current interval. At this point the range
// pos[cur...next) has been searched for a max increasing
// interval. Find a new range that will possibly yield a new
// maximum interval.
// There are a few cases to consider:
//
//
//genome |---+----+------------+------+-----------------------|
// anchors cur cur+1 next next+1
//
// Case 1. The range on the target pos[ cur+1 ... next].t is a
// valid interval (it is roughly the length of the read). In this
// case increase cur and next by 1, and search this range.
//
// genome |---+----+------------+------+-----------------------|
// cur cur+1 next next+1
// read interval ====================
//
// Case 2. The range on the target pos[cur+1 ... next] is not a
// valid interval, and it is much longer than the length of the
// read. This implies that it is impossible to increase the score
// of the read by including both
//
// genome |---+----+--------------------------------+-----+---|
// cur cur+1 next next+1
// read interval ====================
//
// Advance the interval until it includes the next anchor
//
// genome |---+----+------------------+-------------+-----+---|
// cur cur+1 cur+n next next+1
// read interval ====================
//
// First advance pointer in anchor list. If this advances to the
// end, done and no need for further logic checking (break now).
//
// If the next position is not within the same contig as the current,
// advance the current to the next since it is impossible to find
// any more intervals in the current pos.
//
if (curBoundary != nextBoundary) {
cur = next;
curBoundary = nextBoundary;
//
// Start the search for the first interval in the next contig
// just after the current position.
//
if (next < nPos) {
next = cur + 1;
}
}
else {
cur++;
if (cur >= nPos)
break;
//
// Look for need to advance the interval within the same
// contig. If the start of the next match is well past the
// length of this read, keep moving forward matches until it is
// possible to include the next interval in the matches for
// this read.
//
if (params.warp) {
while (cur < next and
next < nPos and
pos[next].t - pos[cur].t >= intervalLength) {
//
// It is impossible to increase the max interval weight any more
// using pos[cur] when pos[next] is too far away from
// pos[cur]. This is because the same set of anchors are used
// when clustering pos[cur+1] ... pos[next] as
// pos[cur] ... pos[next].
// Advance cur until pos[cur] is close enough to matter again.
cur++;
}
}
//
// Advance the next to outside this interval.
next++;
}
if (next > nPos) {
//
// Searched last interval, done.
//
break;
}
//
// Next has advanced. Check what contig it is in.
//
if (next < nPos) {
nextBoundary = ContigStartPos(pos[next].t);
//
// Advance next to the maximum position within this contig that is
// just after where the interval starting at cur is, or the first
// position in the next contig.
//
AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
cur, curBoundary, next, nextBoundary);
}
// if next >= nPos, the boundary stays the same.
//
// When searching multiple contigs, it is important to know the
// boundary of the contig that this anchor is in so that clusters
// do not span multiple contigs. Find the (right hand side)
// boundary of the current contig.
//
curBoundary = ContigStartPos(pos[cur].t);
contigLength = ContigStartPos.Length(pos[cur].t);
//
// Previously tried to advance half. This is being removed since
// proper heuristics are making it not necessary to use.
//
}
return maxLISSize;
}
#endif
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