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clustering.cpp
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#include "clustering.h"
#include <math.h>
#include "crelib/crelib.h"
#include <vector>
#include <unordered_map>
#include <algorithm>
#include <list>
#include <set>
#include <omp.h>
using namespace std;
using namespace cre;
float calcOverlap(float B1, float E1, float B2, float E2)
{
if (B1<=E2 && B1>=B2)
return MIN(E2-B1,E1-B1);
if (E1>=B2 && E1<=E2)
return E1-B2;
if (B2>=B1 && B2<=E1)//1 covers 2
return E2-B2;
else
return -1;
}
/*
PDN=max((E1.End-E1.Begin),(E2.End-E2.Begin))
SDW=0.3
PDW=0.2
ODW=0.5
SampleD=1000# if E1.Sample==E2.Sample else 2
SD=abs((E1.End-E1.Begin)-(E2.End-E2.Begin))/max((E1.End-E1.Begin),(E2.End-E2.Begin))
PD=min(abs(E1.Begin-E2.Begin),abs(E1.End-E2.End))
PD=min(PD,abs((E1.Begin+E1.End)/2-(E2.Begin+E2.End)/2))
PD/=PDN
Overlap=calcOverlap(E1.Begin,E1.End,E2.Begin,E2.End)
OD=Overlap/(max((E1.End-E1.Begin),(E2.End-E2.Begin)))
OD=1-OD
return (SD*SDW+PDW*PD+ODW*OD)*SampleD
*/
float distance(const Signature &A, const Signature &B, bool Partial, float * PPD, Stats BamStats)
{
//if (A.SupportedSV!=B.SupportedSV) return 100;//it shouldn't happen
float SDW, PDW, ODW;
float PDN=900;//TODO: should be realated by tech and type, should make pd>0.5 means not the same
int BP=bestPrecision(A,B),WP=worstPrecision(A,B);
if (WP==2) PDN=30;
else if (WP==0 && BP!=1) PDN=2*(BamStats.Mean+3*BamStats.SD);//should be related with the drp stats
else if (BP==1 && WP==0) PDN=MAX(PDN,2*(BamStats.Mean+3*BamStats.SD));
// SDW=0.33;
// PDW=0.33;
// ODW=0.33;
SDW=1;
PDW=1;
ODW=1;
float SD,PD,OD;
PD=MIN(abs(A.Begin-B.Begin),abs(A.End-B.End));
PD=MIN(PD,abs((A.Begin+A.End)/2-(B.Begin+B.End)/2));
PD/=PDN;
float Overlap=calcOverlap(A.Begin,A.End,B.Begin,B.End);
if (!Partial || precisionLevel(A)==precisionLevel(B))
{
SD=abs(A.Length-B.Length)/MAX(A.Length,B.Length);
OD=Overlap/(MAX((A.End-A.Begin),(B.End-B.Begin)));
OD=1-OD;
}
else
{
const Signature * HighPre, *LowPre;
if (precisionLevel(A)>precisionLevel(B)) {HighPre=&A;LowPre=&B;}
else {HighPre=&B;LowPre=&A;}
SD=abs(HighPre->Length-LowPre->Length)/(HighPre->Length);
OD=Overlap/(HighPre->End-HighPre->Begin);
OD=abs(1-OD);
}
if (PPD!=NULL) *PPD=PD;
if (SD>1) SD=10;
if (PD>1) PD=10;
if (OD>1) OD=10;
return (SD*SDW+PDW*PD+ODW*OD);//+2.0-float(BP);
}
inline int first0(short * A, int S, int B=0)
{
for (int i=B;i<S;++i) if (A==0) return i;
}
bool SigLengthLess(const Signature & a, const Signature &b)
{
if (a.Length<b.Length) return true;
if (a.Length>b.Length) return false;
if (a.Begin<b.Begin) return true;
if (a.Begin>b.Begin) return false;
return a.TemplateName<b.TemplateName;
}
void keepLongestPerRead(vector<Signature> & SignatureCluster)
{
unordered_map<string, Signature> TempsSig;
for (int i=0;i<SignatureCluster.size();++i)
{
if(TempsSig.count(SignatureCluster[i].TemplateName)==0)
{
TempsSig[SignatureCluster[i].TemplateName]=SignatureCluster[i];
}
else if (TempsSig[SignatureCluster[i].TemplateName].Length<SignatureCluster[i].Length)
{
TempsSig[SignatureCluster[i].TemplateName]=SignatureCluster[i];
}
}
SignatureCluster.clear();
for (auto it=TempsSig.begin();it!=TempsSig.end();++it)
{
SignatureCluster.push_back(it->second);
}
}
void simpleClustering(vector<Signature> & SortedSignatures, vector<vector<Signature>> &Clusters, Stats BamStats, bool CuteVer=false)//like jcrd and cuteSV, SortedSignatures may have deleted ones marked by Type=-1
{
if (CuteVer)
{
float MaxDis=200;
// int MinSupport=10;
int MinSupport=0;
for (int i=0;i<SortedSignatures.size();++i)
{
if (SortedSignatures[i].Type==-1) continue;
// printf("%d %d %s\n",SortedSignatures[i].Begin, SortedSignatures[i].Length, SortedSignatures[i].TemplateName.c_str());
if (Clusters.size()==0)
{
Clusters.push_back(vector<Signature>());
}
if (Clusters.back().size()==0) Clusters.back().push_back(SortedSignatures[i]);
else
{
if (SortedSignatures[i].Begin-Clusters.back().back().Begin>MaxDis)
{
if (Clusters.back().size()<MinSupport) Clusters.pop_back();
Clusters.push_back(vector<Signature>());
}
Clusters.back().push_back(SortedSignatures[i]);
}
}
if (Clusters.size()>0 && Clusters.back().size()<MinSupport) Clusters.pop_back();
//add dedup and length segment here
// vector<vector<Signature>> OldCs=Clusters;
// Clusters.clear();
// for (int i=0;i< OldCs.size();++i)
// {
// keepLongestPerRead(OldCs[i]);
// sort(OldCs[i].begin(),OldCs[i].end(),SigLengthLess);
// if (OldCs[i].size()<10) continue;
// double MeanLength=0;
// for (int j=0;j<OldCs[i].size();++j)
// {
// MeanLength+=OldCs[i][j].Length;
// }
// MeanLength/=double(OldCs[i].size());
// double Discrete=0.5*MeanLength;
// Clusters.push_back(vector<Signature>());
// Clusters.back().push_back(OldCs[i][0]);
// int LastLen=OldCs[i][0].Length;
// for (int j=1;j<OldCs[i].size();++j)
// {
// if (OldCs[i][j].Length-LastLen>Discrete)
// {
// Clusters.push_back(vector<Signature>());
// }
// Clusters.back().push_back(OldCs[i][j]);
// LastLen=OldCs[i][j].Length;
// }
// }
}
else
{
float MaxDis=0.7;
int Size=SortedSignatures.size();
short *Clustered=(short*) calloc(sizeof(short),Size);
int F0=0;
while (F0<Size)
{
for (int i=F0;i<SortedSignatures.size();++i)
{
if (Clustered[i]) continue;
if (Clusters.size()==0)
{
Clusters.push_back(vector<Signature>());
}
bool AllLink=true;
for (int j=0;j<Clusters.back().size();++j)
{
float PD;
if (distance(SortedSignatures[i],Clusters.back()[j],true,&PD, BamStats)>MaxDis)//+bestPrecision(SortedSignatures[i],Clusters.back()[j])-2>MaxDis)
{
AllLink=false;
if (PD+bestPrecision(SortedSignatures[i],Clusters.back()[j])-2>MaxDis)
{
Clusters.push_back(vector<Signature>());
Clusters.back().push_back(SortedSignatures[i]);
break;
}
}
}
if (AllLink)
{
Clusters.back().push_back(SortedSignatures[i]);
Clustered[i]=1;
}
}
F0=first0(Clustered,Size,F0);
}
free(Clustered);
}
}
struct ClusterStats
{
double ABegin,AEnd,ALength;
set<string> Templates;
ClusterStats():ABegin(0),AEnd(0),ALength(0),Templates(){}
};
bool isBrother(const Signature &A, const Signature &B, float PosRatio=0.1, int ForceBrother=5, float LengthRatio=0.1, int LengthMinEndurance=5, int ForceBrother2=5, float LengthRatio2=0.1, int NearRange=500, const ClusterStats * AS=nullptr, const ClusterStats* BS=nullptr)
{
// if (SupportedSV==3)//Inv
// {
// if (A.InvLeft && B.InvLeft && A.InvRight && B.InvRight) return isBrother(A,B,0,Ratio,ForceBrother);
// if (A.InvLeft && B.InvLeft)
// {
// if ((!A.InvRight) && (!B.InvRight))
// {
// if (abs(A.Begin-B.Begin)<=ForceBrother) return true;
// return false;
// }
// else if (!A.InvRight)
// {
// if (abs(A.Begin-B.Begin)<=ForceBrother && (abs(A.End-B.End)<=ForceBrother || B.Length>=A.Length)) return true;
// return false;
// }
// else if (!B.InvRight)
// {
// if (abs(A.Begin-B.Begin)<=ForceBrother && (abs(A.End-B.End)<=ForceBrother || A.Length>=B.Length)) return true;
// return false;
// }
// }
// if (A.InvRight && B.InvRight)
// {
// if ((!A.InvLeft) && (!B.InvLeft))
// {
// if (abs(A.End-B.End)<=ForceBrother) return true;
// return false;
// }
// else if (!A.InvLeft)
// {
// if (abs(A.End-B.End)<=ForceBrother && (abs(A.End-B.End)<=ForceBrother || B.Length>=A.Length)) return true;
// return false;
// }
// else if (!B.InvLeft)
// {
// if (abs(A.End-B.End)<=ForceBrother && (abs(A.End-B.End)<=ForceBrother || A.Length>=B.Length)) return true;
// return false;
// }
// }
// }
// if (A.Type==1 || B.Type==1)
// {
// if (A.Type==1)
// {
// if (A.Begin-ForceBrother<=B.Begin && A.Begin>MIN(B.Begin-ForceBrother,B.Begin-MinLength*Ratio) && A.End+ForceBrother>=B.End && A.End<MAX(B.End+ForceBrother,B.End+MinLength*Ratio)) return true;
// }
// if (B.Type==1)
// {
// if (B.Begin-ForceBrother<=A.Begin && A.Begin>MIN(A.Begin-ForceBrother,A.Begin-MinLength*Ratio) && B.End+ForceBrother>=A.End && B.End<MAX(A.End+ForceBrother,A.End+MinLength*Ratio)) return true;
// }
// return false;
// }
if (A.TemplateName==B.TemplateName) return false;
if (abs(A.Begin-B.Begin)<=ForceBrother && abs(A.End-B.End)<=ForceBrother) return true;
int MinLength=min(A.Length,B.Length);
int LengthEndurance=max(LengthMinEndurance,int(MinLength*LengthRatio));
if (abs(A.Begin-B.Begin)<=MinLength*PosRatio && abs(A.End-B.End)<=MinLength*PosRatio && abs(A.Length-B.Length)<=LengthEndurance) return true;
return false;
}
bool isBrother(const Signature* A, const Signature* B, float PosRatio=0.1, int ForceBrother=5, float LengthRatio=0.1, int LengthMinEndurance=5, int ForceBrother2=5, float LengthRatio2=0.1, int NearRange=500, const ClusterStats * AS=nullptr, const ClusterStats* BS=nullptr)
{
return isBrother(*A, *B, PosRatio, ForceBrother, LengthRatio, LengthMinEndurance, ForceBrother2, LengthRatio2, NearRange, AS, BS);
}
bool isBrother(const vector<Signature> &A, const vector<Signature> &B, float PosRatio=0.1, int ForceBrother=5, float LengthRatio=0.1, int LengthMinEndurance=5, int ForceBrother2=5, float LengthRatio2=0.1, int NearRange=500, const ClusterStats * AS=nullptr, const ClusterStats* BS=nullptr)
{
if (A[0].SupportedSV!=B[0].SupportedSV) return false;
NearRange=200;
if (A.size()==1 && B.size()==1)
{
if (abs(A[0].Length-B[0].Length)<ForceBrother2 && abs(A[0].Begin-B[0].Begin)<NearRange && abs(A[0].End-B[0].End)<NearRange) return true;
return false;
}
const set<string> & ATemplates=AS->Templates;
double MeanLength=(AS->ALength+BS->ALength)/2.0;
double LengthDiff=ForceBrother2;
double LengthRatioDiff=LengthRatio2;
double MinSize=MIN(A.size(),B.size());
LengthDiff/=MinSize;
LengthRatioDiff/=MinSize;
if (abs(AS->ABegin-BS->ABegin)<NearRange && abs(AS->AEnd-BS->AEnd)<NearRange && (((abs(AS->ALength-MeanLength)/MeanLength)<LengthRatioDiff)||(abs(AS->ALength-BS->ALength)<LengthDiff)))
{
for (int i=0;i<B.size();++i)
{
if (ATemplates.count(B[i].TemplateName)!=0) return false;//has sigs from same template, no brother
}
return true;
}
return false;
}
inline int getSupportedSV(const vector<Signature> & Cluster)
{
return Cluster[0].SupportedSV;
}
inline int getSupportedSV(const vector<Signature*> & Cluster)
{
return Cluster[0]->SupportedSV;
}
inline int getSupportedSV(const vector<vector<Signature>> & Cluster)
{
return Cluster[0][0].SupportedSV;
}
void setValues(Signature & S, unsigned& MinBegin, unsigned& MaxBegin, unsigned& MinEnd, unsigned & MaxEnd, unsigned& SignatureCount, vector<ClusterStats>& CStats)
{
MinBegin=S.Begin;
MaxBegin=S.Begin;
MinEnd=S.End;
MaxEnd=S.End;
SignatureCount=1;
CStats.push_back(ClusterStats());
}
void setValues(Signature* & S, unsigned& MinBegin, unsigned& MaxBegin, unsigned& MinEnd, unsigned & MaxEnd, unsigned& SignatureCount, vector<ClusterStats>& CStats)
{
setValues(*S, MinBegin, MaxBegin, MinEnd, MaxEnd, SignatureCount, CStats);
}
void setValues(vector<Signature> & Ss, unsigned& MinBegin, unsigned& MaxBegin, unsigned& MinEnd, unsigned & MaxEnd, unsigned& SignatureCount, vector<ClusterStats>& CStats)
{
ClusterStats CS;
MinBegin=Ss[0].Begin;
MaxBegin=Ss[0].Begin;
MinEnd=Ss[0].End;
MaxEnd=Ss[0].End;
for (int i=0;i<Ss.size();++i)
{
Signature & S=Ss[i];
MinBegin=MIN(MinBegin,S.Begin);
MaxBegin=MAX(MaxBegin,S.Begin);
MinEnd=MIN(MinEnd,S.End);
MaxEnd=MAX(MaxEnd,S.End);
CS.ABegin=(CS.ABegin*i)/(i+1)+Ss[i].Begin/(double(i+1));
CS.AEnd=(CS.AEnd*i)/(i+1)+Ss[i].End/(double(i+1));
CS.ALength=(CS.ALength*i)/(i+1)+Ss[i].Length/(double(i+1));
CS.Templates.insert(Ss[i].TemplateName);
}
CStats.push_back(CS);
SignatureCount=Ss.size();
}
template<typename T> class Brotherhood
{
public:
vector<T> Cluster;
bool CCS;
unsigned int MinBegin, MaxBegin, MinEnd, MaxEnd, SignatureCount;
vector<ClusterStats> CStats;
Brotherhood(bool IsCCS=false):Cluster(),MinBegin(0),MaxEnd(0),CCS(IsCCS) {};
Brotherhood(T &S, bool IsCCS=false):Cluster(),MinBegin(0),MaxEnd(0),CCS(IsCCS) {setCluster(S);};
void setCluster(T & S)
{
Cluster.clear();
Cluster.push_back(S);
setValues(S,MinBegin, MaxBegin, MinEnd, MaxEnd, SignatureCount,CStats);
}
bool canMerge(const Brotherhood<T> & Other, Arguments &Args) const
{
int SupportedSV=getSupportedSV(Cluster);
int ForceBrother=Args.BrotherhoodTypeForceBrothers[SupportedSV];
float Ratio=Args.BrotherhoodTypeRatios[SupportedSV];
// Ratio=1.5-Args.TotalCoverage*0.3;
// Ratio=max(0.2f,Ratio);
int LengthMinEndurance=Args.BrotherhoodTypeLengthMinEndurance[SupportedSV];
float LengthRatio=Args.BrotherhoodTypeLengthRatios[SupportedSV];
int NearRange=Args.BrotherhoodNearRanges[SupportedSV];
int ForceBrother2=Args.BrotherhoodTypeForceBrothers2[SupportedSV];
float LengthRatio2=Args.BrotherhoodTypeLengthRatios2[SupportedSV];
if (CCS)
{
ForceBrother=Args.BrotherhoodCCSTypeForceBrothers[SupportedSV];
Ratio=Args.BrotherhoodCCSTypeRatios[SupportedSV];
}
// fprintf(stderr,"%d %d %d %d %d %d %d\n",Other.MinBegin-MaxEnd, Other.MinBegin, MaxEnd, MinBegin-Other.MaxEnd,MinBegin, Other.MaxEnd,Brotherhood::ForceBrother);
if (((Other.MinBegin>MaxEnd+ForceBrother+NearRange) || ((MinBegin>Other.MaxEnd+ForceBrother+NearRange)))) return false;
// fprintf(stderr,"yes");
for (int i=0;i<Cluster.size();++i)
{
const T & A=Cluster[i];
for (int j=0;j<Other.Cluster.size();++j)
{
const T & B=Other.Cluster[j];
if (isBrother(A,B,Ratio,ForceBrother,LengthRatio,LengthMinEndurance,ForceBrother2,LengthRatio2,NearRange,&(CStats[i]),&(Other.CStats[j])))
{
return true;
}
}
}
return false;
}
bool merge(Brotherhood<T> & Other, Arguments &Args)
{
if (canMerge(Other,Args))
{
for (T & B:Other.Cluster)
{
Cluster.push_back(B);
}
MinBegin=min(MinBegin,Other.MinBegin);
MaxBegin=MAX(MaxBegin,Other.MaxBegin);
MinEnd=MIN(MinEnd,Other.MinEnd);
MaxEnd=max(MaxEnd,Other.MaxEnd);
SignatureCount+=Other.SignatureCount;
CStats.insert(CStats.end(),make_move_iterator(Other.CStats.begin()),make_move_iterator(Other.CStats.end()));
return true;
}
return false;
}
};
template<typename T> void brotherClusteringList(list<Brotherhood<T>> &Brotherhoods, Arguments &Args)
{
int Round=0;
while (1)
{
// fprintf(stderr,"Round%d: %lu\n",Round,Brotherhoods.size());
++Round;
Brotherhoods.sort([](Brotherhood<T> & a, Brotherhood<T> &b)-> bool {return a.MinBegin<b.MinBegin;});
bool Next=false;
for (auto Ai=Brotherhoods.begin();Ai!=Brotherhoods.end();++Ai)
{
for (auto Bi=next(Ai);Bi!=Brotherhoods.end();++Bi)
{
if (Ai->MaxEnd+MIN(Args.ClusteringMaxMergeRange,0.5*(Ai->MaxEnd-Ai->MinBegin))<Bi->MinBegin) break;
if (Ai->merge(*Bi,Args))
{
Brotherhoods.erase(Bi);
Next=true;
break;
}
}
}
if (!Next) break;
}
Brotherhoods.sort([](Brotherhood<T> & a, Brotherhood<T> &b)-> bool {return a.MinBegin<b.MinBegin;});
}
template<typename T> void brotherClustering(vector<T> & SortedTs, list<Brotherhood<T>>& Brotherhoods, Stats BamStats, Arguments &Args)
{
//Need improve 1 thread efficiency for large size
if (/*Args.ThreadN==1 || */SortedTs.size()<=Args.ClusteringBatchSize*1.1)
{
for (T & S:SortedTs) Brotherhoods.push_back(Brotherhood<T>(S,Args.AllCCS));
brotherClusteringList(Brotherhoods,Args);
}
else
{
vector<list<Brotherhood<T>>> BatchBrotherhoods;
for (int i=0;i<SortedTs.size();++i)
{
if (i%Args.ClusteringBatchSize==0) BatchBrotherhoods.push_back(list<Brotherhood<T>>());
BatchBrotherhoods[BatchBrotherhoods.size()-1].push_back(Brotherhood<T>(SortedTs[i],Args.AllCCS));
}
// #pragma omp parallel for
for (int i=0;i<BatchBrotherhoods.size();++i)
{
brotherClusteringList(BatchBrotherhoods[i],Args);
}
// for (int i=0;i<BatchBrotherhoods.size();++i)
// {
// Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
// }
// brotherClusteringList(Brotherhoods,Args);
vector<list<Brotherhood<T>>> Edges;
for (int i=0;i<BatchBrotherhoods.size()-1;++i)
{
int Left,Right;
Left=BatchBrotherhoods[i+1].front().MinBegin-Args.ClusteringMaxMergeRange;
Right=BatchBrotherhoods[i].back().MaxBegin+Args.ClusteringMaxMergeRange;
auto LeftMost=BatchBrotherhoods[i].begin();
if (i!=0) advance(LeftMost,unsigned(BatchBrotherhoods[i].size()/2.0));
auto RightMost=BatchBrotherhoods[i+1].end();
if (i+1!=BatchBrotherhoods.size()-1)
{
RightMost=BatchBrotherhoods[i+1].begin();
advance(RightMost,unsigned(BatchBrotherhoods[i+1].size()/2.0));
}
Edges.push_back(list<Brotherhood<T>>());
typename list<Brotherhood<T>>::iterator LeftIter=BatchBrotherhoods[i].end();
--LeftIter;
typename list<Brotherhood<T>>::iterator RightIter=BatchBrotherhoods[i+1].begin();
for (;LeftIter!=LeftMost;--LeftIter)
{
if (LeftIter->MaxBegin<Left) break;
if (LeftIter==LeftMost)
{
if (i!=0 && !(LeftIter->MaxBegin<Left))
Args.Log.verbose("Risk of not fully clustered detected.");//Change batch size to sig count related to avoid? Or, can be avoided by extend the boundaries. The influence is trivial, so it's not urgent to solve it.
break;
}
}
for (;RightIter!=RightMost;++RightIter)
{
if (RightIter->MinBegin>Right) break;
}
if (RightIter==RightMost && i+1!=BatchBrotherhoods.size()-1)
Args.Log.verbose("Risk of not fully clustered detected.");
Edges[Edges.size()-1].splice(Edges[Edges.size()-1].end(),BatchBrotherhoods[i],LeftIter,BatchBrotherhoods[i].end());
Edges[Edges.size()-1].splice(Edges[Edges.size()-1].end(),BatchBrotherhoods[i+1],BatchBrotherhoods[i+1].begin(),RightIter);
// Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
}
// #pragma omp parallel for
for (int i=0;i<Edges.size();++i)
{
brotherClusteringList(Edges[i],Args);
}
for (int i=0;i<BatchBrotherhoods.size();++i)
{
Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
}
for (int i=0;i<Edges.size();++i)
{
Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(Edges[i].begin()),make_move_iterator(Edges[i].end()));
}
Brotherhoods.sort([](Brotherhood<T> & a, Brotherhood<T> &b)-> bool {return a.MinBegin<b.MinBegin;});
}
}
//To reduce memory usage
template<typename T> void brotherClustering(vector<T> & SortedTs, list<Brotherhood<T*>>& Brotherhoods, Stats BamStats, Arguments &Args)
{
T* PT;
//Need improve 1 thread efficiency for large size
if (/*Args.ThreadN==1 || */SortedTs.size()<=Args.ClusteringBatchSize*1.1)
{
for (T & S:SortedTs)
{
PT=&S;
Brotherhoods.push_back(Brotherhood<T*>(PT,Args.AllCCS));
}
brotherClusteringList(Brotherhoods,Args);
}
else
{
vector<list<Brotherhood<T*>>> BatchBrotherhoods;
for (int i=0;i<SortedTs.size();++i)
{
if (i%Args.ClusteringBatchSize==0) BatchBrotherhoods.push_back(list<Brotherhood<T*>>());
PT=&SortedTs[i];
BatchBrotherhoods[BatchBrotherhoods.size()-1].push_back(Brotherhood<T*>(PT,Args.AllCCS));
}
// #pragma omp parallel for
for (int i=0;i<BatchBrotherhoods.size();++i)
{
brotherClusteringList(BatchBrotherhoods[i],Args);
}
// for (int i=0;i<BatchBrotherhoods.size();++i)
// {
// Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
// }
// brotherClusteringList(Brotherhoods,Args);
vector<list<Brotherhood<T*>>> Edges;
for (int i=0;i<BatchBrotherhoods.size()-1;++i)
{
int Left,Right;
Left=BatchBrotherhoods[i+1].front().MinBegin-Args.ClusteringMaxMergeRange;
Right=BatchBrotherhoods[i].back().MaxBegin+Args.ClusteringMaxMergeRange;
auto LeftMost=BatchBrotherhoods[i].begin();
if (i!=0) advance(LeftMost,unsigned(BatchBrotherhoods[i].size()/2.0));
auto RightMost=BatchBrotherhoods[i+1].end();
if (i+1!=BatchBrotherhoods.size()-1)
{
RightMost=BatchBrotherhoods[i+1].begin();
advance(RightMost,unsigned(BatchBrotherhoods[i+1].size()/2.0));
}
Edges.push_back(list<Brotherhood<T*>>());
typename list<Brotherhood<T*>>::iterator LeftIter=BatchBrotherhoods[i].end();
--LeftIter;
typename list<Brotherhood<T*>>::iterator RightIter=BatchBrotherhoods[i+1].begin();
for (;LeftIter!=LeftMost;--LeftIter)
{
if (LeftIter->MaxBegin<Left) break;
if (LeftIter==LeftMost)
{
if (i!=0 && !(LeftIter->MaxBegin<Left))
Args.Log.verbose("Risk of not fully clustered detected.");//Change batch size to sig count related to avoid? Or, can be avoided by extend the boundaries. The influence is trivial, so it's not urgent to solve it.
break;
}
}
for (;RightIter!=RightMost;++RightIter)
{
if (RightIter->MinBegin>Right) break;
}
if (RightIter==RightMost && i+1!=BatchBrotherhoods.size()-1)
Args.Log.verbose("Risk of not fully clustered detected.");
Edges[Edges.size()-1].splice(Edges[Edges.size()-1].end(),BatchBrotherhoods[i],LeftIter,BatchBrotherhoods[i].end());
Edges[Edges.size()-1].splice(Edges[Edges.size()-1].end(),BatchBrotherhoods[i+1],BatchBrotherhoods[i+1].begin(),RightIter);
// Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
}
// #pragma omp parallel for
for (int i=0;i<Edges.size();++i)
{
brotherClusteringList(Edges[i],Args);
}
for (int i=0;i<BatchBrotherhoods.size();++i)
{
Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(BatchBrotherhoods[i].begin()),make_move_iterator(BatchBrotherhoods[i].end()));
}
for (int i=0;i<Edges.size();++i)
{
Brotherhoods.insert(Brotherhoods.end(),make_move_iterator(Edges[i].begin()),make_move_iterator(Edges[i].end()));
}
Brotherhoods.sort([](Brotherhood<T*> & a, Brotherhood<T*> &b)-> bool {return a.MinBegin<b.MinBegin;});
}
}
void brotherClustering(vector<Signature> & SortedSignatures, vector<vector<Signature>> &Clusters, Stats BamStats, Arguments &Args)
{
list<Brotherhood<Signature*>> Brotherhoods;
brotherClustering(SortedSignatures,Brotherhoods,BamStats,Args);
for (Brotherhood<Signature*>& B :Brotherhoods)
{
Clusters.push_back(vector<Signature>());
for (int i=0;i<B.Cluster.size();++i) Clusters.back().push_back(move(*B.Cluster[i]));
}
}
//May duplicate some signatures.
void fitInClusters(vector<vector<Signature>> &Clusters, vector<Signature> & OtherSignatures, vector<Signature> &Leftovers, Arguments& Args)
{
vector<bool> Merged;
for (int i=0;i<OtherSignatures.size();++i) Merged.push_back(false);
for (vector<Signature>& Cluster : Clusters)
{
int ForceBrother=Args.BrotherhoodTypeForceBrothers[Cluster[0].SupportedSV];
float Ratio=Args.BrotherhoodTypeRatios[Cluster[0].SupportedSV];
int LengthMinEndurance=Args.BrotherhoodTypeLengthMinEndurance[Cluster[0].SupportedSV];
float LengthRatio=Args.BrotherhoodTypeLengthRatios[Cluster[0].SupportedSV];
double ClusterSize=Cluster.size();
double SupportedBrother=0;
for (int i=0;i<OtherSignatures.size();++i)
{
SupportedBrother=0;
for (const Signature & s: Cluster)
{
if (isBrother(s, OtherSignatures[i],Ratio,ForceBrother,LengthRatio,LengthMinEndurance))
{
SupportedBrother+=1;
if (SupportedBrother/ClusterSize>=0.8)
{
Cluster.push_back(OtherSignatures[i]);
Merged[i]=true;
break;
}
}
}
}
}
for (int i=0;i<OtherSignatures.size();++i)
{
if (!Merged[i]) Leftovers.push_back(OtherSignatures[i]);
}
}
void batchClustering(vector<Signature> & SortedSignatures, vector<vector<Signature>> &Clusters, Stats BamStats, Arguments& Args)
{
vector<Signature> BaseSignatures,OtherSignatures;
vector<double> Qualities;
for (int i=0;i<SortedSignatures.size();++i)
{
Qualities.push_back(SortedSignatures[i].Quality);
}
sort(Qualities.data(),Qualities.data()+Qualities.size());
double Quantile=0;
if (Qualities.size()!=0) Quantile=Qualities[int(Qualities.size()*0.2)];
for (int i=0;i<SortedSignatures.size();++i)
{
if (SortedSignatures[i].Quality>=Quantile) BaseSignatures.push_back(SortedSignatures[i]);
else OtherSignatures.push_back(SortedSignatures[i]);
}
brotherClustering(BaseSignatures,Clusters,BamStats,Args);
vector<Signature> Leftovers;
fitInClusters(Clusters, OtherSignatures, Leftovers, Args);
fprintf(stderr, "Quantile: %lf, Base: %ld, Other: %ld, Leftover: %ld\n",Quantile, BaseSignatures.size(),OtherSignatures.size(),Leftovers.size());
// brotherClustering(Leftovers,Clusters,BamStats,Args);
}
void mergeClusters(vector<vector<Signature>> &Clusters, Stats BamStats, Arguments& Args)
{
for (int i=0;i<Clusters.size();++i)
{
if (Clusters[i].size()==0) continue;
for (int j=0;j<Clusters.size();++j)
{
if (j==i) continue;
if (Clusters[j].size()==0) continue;
if(isBrother(Clusters[i],Clusters[j]))
{
Clusters[i].insert(Clusters[i].end(),make_move_iterator(Clusters[j].begin()),make_move_iterator(Clusters[j].end()));
if(Clusters[j].size()!=0) Clusters[j].clear();
}
}
}
}
inline void addSigMap(unordered_map<string,list<list<Brotherhood<Signature>>::iterator>> &PotentialMerges, list<Brotherhood<Signature>>::iterator & Iter)
{
if (PotentialMerges.count(Iter->Cluster[0].TemplateName)==0) PotentialMerges[Iter->Cluster[0].TemplateName]=list<list<Brotherhood<Signature>>::iterator>();
list<list<Brotherhood<Signature>>::iterator>& TheList=PotentialMerges[Iter->Cluster[0].TemplateName];
TheList.push_back(Iter);
// TheList.splice(TheList.end(),SignatureBrotherhoods,Iter);
// Iter=PreviousIter;
}
inline void addSigMap(unordered_map<string,list<list<Signature>::iterator>> &PotentialMerges, list<Signature>::iterator & Iter)
{
if (PotentialMerges.count(Iter->TemplateName)==0) PotentialMerges[Iter->TemplateName]=list<list<Signature>::iterator>();
list<list<Signature>::iterator>& TheList=PotentialMerges[Iter->TemplateName];
TheList.push_back(Iter);
// TheList.splice(TheList.end(),SignatureBrotherhoods,Iter);
// Iter=PreviousIter;
}
inline unsigned getBegin(list<list<Brotherhood<Signature>>::iterator>::iterator & Iter)
{
return (*Iter)->MinBegin;
}
inline unsigned getEnd(list<list<Brotherhood<Signature>>::iterator>::iterator & Iter)
{
return (*Iter)->MaxEnd;
}
inline unsigned getBegin(list<Brotherhood<Signature>>::iterator & Iter)
{
return Iter->MinBegin;
}
inline unsigned getEnd(list<Brotherhood<Signature>>::iterator & Iter)
{
return Iter->MaxEnd;
}
inline unsigned getBegin(list<list<Signature>::iterator>::iterator & Iter)
{
return (*Iter)->Begin;
}
inline unsigned getEnd(list<list<Signature>::iterator>::iterator & Iter)
{
return (*Iter)->End;
}
inline unsigned getBegin(list<Signature>::iterator & Iter)
{
return Iter->Begin;
}
inline unsigned getEnd(list<Signature>::iterator & Iter)
{
return Iter->End;
}
inline unsigned getSupportedSV(const list<list<Brotherhood<Signature>>::iterator>::iterator & Iter)
{
return (*Iter)->Cluster[0].SupportedSV;
}
inline unsigned getSupportedSV(const list<list<Signature>::iterator>::iterator & Iter)
{
return (*Iter)->SupportedSV;
}
inline unsigned getSupportedSV(const list<Signature>::iterator & Iter)
{
return Iter->SupportedSV;
}
//All Brotherhoods in Sigs have only one Signature.
//Can be DP optimized.
template<typename TypeIterType> bool BestFit(list<TypeIterType> &Sigs, double Begin, double End, typename list<TypeIterType>::iterator &FitBegin, typename list<TypeIterType>::iterator &FitEnd, unsigned &FitLength)
{
int SupportedSV=getSupportedSV(Sigs.begin());
int MaxBeginDiff=1000000;
double LengthEndureMin=10;
double LengthEndureRatio=0.1;
if (SupportedSV==1)
{
MaxBeginDiff=200;
LengthEndureRatio=1.0;
}
double Length=End-Begin;
double LengthMin=MIN(Length-LengthEndureMin,Length*(1.0-LengthEndureRatio));
double LengthMax=MAX(Length+LengthEndureMin,Length*(1.0+LengthEndureRatio));
Sigs.sort([](TypeIterType & a, TypeIterType &b)-> bool {return getBegin(a)<getBegin(b);});
unsigned MinDiff=0xffffffff;
unsigned MinDiffMergeCount=0;
unsigned MergeCount=0;
for (auto Iter=Sigs.begin();Iter!=Sigs.end();++Iter)
{
double LengthAdd=getEnd(Iter)-getBegin(Iter);
double ThisBegin=getBegin(Iter);
double ThisEnd=getEnd(Iter);
MergeCount=1;
for (auto Jter=Iter;Jter!=Sigs.end();++Jter)
{
if (Jter==Iter) continue;
if (abs(getBegin(Jter)-ThisBegin)<MaxBeginDiff)
{
if (getBegin(Jter)>ThisBegin) break;
continue;
}
LengthAdd+=getEnd(Jter)-getBegin(Jter);
ThisEnd=ThisBegin+LengthAdd;
++MergeCount;
if (LengthAdd>=LengthMin && LengthAdd<=LengthMax)
{
unsigned Diff=ThisBegin-Begin+ThisEnd-End;
if (Diff<MinDiff)
{
MinDiff=Diff;
MinDiffMergeCount=MergeCount;
FitBegin=Iter;
FitEnd=Jter;
FitLength=LengthAdd;
++FitEnd;
}
}
}
}
if (MinDiff<200) return true;
return false;
}
void mergeAdjacent(list<Brotherhood<Signature>> &SignatureBrotherhoods, Arguments & Args)//deprecated
{
int Range=500;
int MaxMergeLength=2000000;
list<Brotherhood<Signature>> MergeCandidates;
for (auto Iter=SignatureBrotherhoods.begin();Iter!=SignatureBrotherhoods.end();++Iter)
{
if ((Iter->MinEnd-Iter->MinBegin)<=MaxMergeLength)
{
list<Brotherhood<Signature>>::iterator PreviousIter=Iter;
--PreviousIter;
MergeCandidates.splice(MergeCandidates.end(),SignatureBrotherhoods,Iter);
Iter=PreviousIter;
}
}
fprintf(stderr,"Brotherhoods:%lu , merge candidates:%lu\n",SignatureBrotherhoods.size()+MergeCandidates.size(),MergeCandidates.size());
list<Brotherhood<Signature>> NewBros;
unsigned Merged=0;
for (auto Iter=MergeCandidates.begin();Iter!=MergeCandidates.end();++Iter)
{
if ((Iter->MinEnd-Iter->MinBegin)<50) continue;
unsigned SearchLeft=Iter->MinBegin-Range;
unsigned SearchRight=Iter->MaxEnd+Range;
unordered_map<string,list<list<Brotherhood<Signature>>::iterator>> PotentialMerges;
for (auto Jter=Iter;Jter!=MergeCandidates.end();++Jter)
{
if (Jter==Iter) continue;
if (Jter->MinBegin>SearchRight) break;
if (Jter->SignatureCount==1)
{
// list<Brotherhood<Signature>>::iterator PreviousIter=Jter;
// --PreviousIter;
// addSigMap(PotentialMerges,MergeCandidates,Jter,PreviousIter);
addSigMap(PotentialMerges,Jter);
}
}
for (auto Jter=Iter;true;--Jter)
{
if (Jter==Iter)
{
if (Jter==MergeCandidates.begin()) break;
continue;
}
if (Jter->MinBegin<SearchLeft) break;
if (Jter->SignatureCount==1)
{
addSigMap(PotentialMerges,Jter);
}
if (Jter==MergeCandidates.begin()) break;
}
list<list<Brotherhood<Signature>>::iterator>::iterator FitBegin, FitEnd;
unsigned FitLength;
for (auto mi=PotentialMerges.begin();mi!=PotentialMerges.end();++mi)
{
if (BestFit(mi->second,Iter->MinBegin,Iter->MinEnd,FitBegin,FitEnd,FitLength))
{
Signature NewSig((*FitBegin)->Cluster[0]);
NewSig.End=NewSig.Begin+FitLength;
NewSig.Length=FitLength;
if (NewSig.SupportedSV==1)
{
NewSig.InsBases="";
}
for (auto I=FitBegin;I!=FitEnd;++I)
{
NewSig.InsBases+=(*I)->Cluster[0].InsBases;
MergeCandidates.erase((*I));
}
Brotherhood<Signature> NewBro(NewSig,(*FitBegin)->CCS);
if (!Iter->merge(NewBro,Args))
{
NewBros.push_back(NewBro);
}
else
{
++Merged;
}
// mi->second.erase(FitBegin,FitEnd);
}
}
// for (auto mi=PotentialMerges.begin();mi!=PotentialMerges.end();++mi)
// {
// NewBros.splice(NewBros.end(),mi->second);
// }
}
fprintf(stderr,"NewBros:%lu, Merged:%lu\n",NewBros.size(),Merged);
MergeCandidates.splice(MergeCandidates.end(),NewBros);
SignatureBrotherhoods.splice(SignatureBrotherhoods.end(),MergeCandidates);
SignatureBrotherhoods.sort([](Brotherhood<Signature> & a, Brotherhood<Signature> &b)-> bool {return a.MinBegin<b.MinBegin;});
}
//Merge adjacent sigs that not clustered in the first clustering and add to brotherhoods for the next step
//Will change ClusteredBrotherhoods. Will not change SortedSignatures.
void genMergedSigs(list<Brotherhood<Signature>> &ClusteredBrotherhoods, vector<Signature> & SortedSignatures, int *ClusterCount, Stats BamStats, Arguments & Args)
{
for (Brotherhood<Signature>& C : ClusteredBrotherhoods)
{
for (int i=0;i<C.Cluster.size();++i) ClusterCount[C.Cluster[i].ID]=C.Cluster.size();
}
unordered_map<string,vector<vector<Signature>::iterator>> TemplateSigs;
vector<Signature> Sigs=SortedSignatures;
int SupportedSV=0;
if (Sigs.size()>0) SupportedSV=Sigs[0].SupportedSV;
for (int i=0;i<SortedSignatures.size();++i)
{
if (ClusterCount[SortedSignatures[i].ID]>1) continue;
if (TemplateSigs.count(SortedSignatures[i].TemplateName)==0) TemplateSigs[SortedSignatures[i].TemplateName]=vector<vector<Signature>::iterator>();
TemplateSigs[SortedSignatures[i].TemplateName].push_back(SortedSignatures.begin()+i);
}
if (SupportedSV!=1)
{
int Endurance=200;
for (auto mi=TemplateSigs.begin();mi!=TemplateSigs.end();++mi)
{
sort(mi->second.begin(),mi->second.end(),[](vector<Signature>::iterator & a, vector<Signature>::iterator &b)-> bool {return a->Begin<b->Begin;});
int NewBegin=mi->second[0]->Begin;
int Merged=0;
string NewInsBases="";
for (int i=1;i<mi->second.size();++i)
{
Signature &Former=*mi->second[i-1];
Signature &Latter=*mi->second[i];
if (Latter.Begin>=Former.End && Latter.Begin<Former.End+Endurance)
{
++Merged;
NewInsBases+=Latter.InsBases;
}
else
{
Signature NewSig(Latter.Type,Latter.Tech,Latter.SupportedSV,NewBegin,Latter.End,Latter.TemplateName,Latter.Quality,NewInsBases.c_str());
NewSig.Artificial=true;
if (Merged>0) Sigs.push_back(NewSig);
Merged=0;
NewInsBases="";
NewBegin=Latter.Begin;
}
}
}
}
else
{
int Endurance=500;
for (auto mi=TemplateSigs.begin();mi!=TemplateSigs.end();++mi)
{
sort(mi->second.begin(),mi->second.end(),[](vector<Signature>::iterator & a, vector<Signature>::iterator &b)-> bool {return a->Begin<b->Begin;});
int NewBegin=mi->second[0]->Begin;
int Merged=0;