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#include "SpliceGraph.h"
#include "sjAlignSplit.h"
#include "ReadAlign.h"
void SpliceGraph::findSuperTr(const char *readSeq, const char *readSeqRevCompl, const uint32 readLen, const string &readName, Genome &mapGen)
{//find the candidate superTranscripts: seed-and-rank algorithm implemented
//hardcoded for now
float seedCoverageThreshold = 0.02;
float seedCoverageMinToMax = 0.5;
uint32 seedMultMax = P.seedMultimapNmax;
uint32 seedSpacing = 1;
uint32 seedLen=mapGen.pGe.gSAindexNbases; //TODO: make user-definable vector<uint32> seedSuperTr;
vector<uint32> seedSuperTr;
seedSuperTr.reserve(seedMultMax);
memset(superTrSeedCount,0,sizeof(superTrSeedCount[0])*2*superTrome.N);
for (uint32 iseed=0; iseed<readLen; iseed+=seedSpacing) {//loop through seeds
//calculate index
uint64 ind1=0;
for (uint32 ii=iseed; ii<iseed+seedLen; ii++) {
uint b=(uint64) readSeq[ii];
if (b>3) {//N
continue; //no mapping for seeds with Ns
} else {
ind1 <<= 2;
ind1 += b;
};
};
//find seed boundaries in SA
uint64 iSA1=mapGen.SAi[mapGen.genomeSAindexStart[seedLen-1]+ind1]; // starting point for suffix array search.
if ( (iSA1 & mapGen.SAiMarkAbsentMaskC) != 0) {//prefix does not exist, skip this seed
continue;
};
uint64 iSA2;
if (mapGen.genomeSAindexStart[seedLen-1]+ind1+1 < mapGen.genomeSAindexStart[seedLen]) {//we are not at the end of the SA
iSA2=((mapGen.SAi[mapGen.genomeSAindexStart[seedLen-1]+ind1+1] & mapGen.SAiMarkNmask) & mapGen.SAiMarkAbsentMask) - 1;
} else {
iSA2=mapGen.nSA-1;
};
if (iSA2-iSA1>=seedMultMax) //this seed map too many times
continue;
seedSuperTr.clear();
seedSuperTr.resize(iSA2-iSA1+1);
for (uint64 isa=iSA1;isa<=iSA2;isa++) {//loop through seed SA boundaries
uint64 a1 = mapGen.SA[isa];
uint64 aStr = a1 >> mapGen.GstrandBit;
a1 = a1 & mapGen.GstrandMask; //remove strand bit
if (aStr==1)
a1 = mapGen.nGenome - (seedLen+a1);
if (a1>=mapGen.sjGstart) {//this is sj align. Probably do not need it...
uint64 a1D, aLengthD, a1A, aLengthA, sj1;
if ( sjAlignSplit(a1, seedLen, mapGen, a1D, aLengthD, a1A, aLengthA, sj1) ) {//if align crosses the junction, replace a1 with a1D
a1=a1D;
} else {
continue;//this align does not cross the junction, no need to contine
};
};
seedSuperTr[isa-iSA1]=(uint32)(aStr*superTrome.N + mapGen.chrBin[a1 >> mapGen.pGe.gChrBinNbits]);
};//loop through seed SA boundaries
sort(seedSuperTr.begin(),seedSuperTr.end());
uint32 su1prev=(uint32)-1;
for (auto &su1 : seedSuperTr) {//this will eliminate multiple matches of the same seed into the same suTr
if (su1!=su1prev) {
superTrSeedCount[su1]++;
su1prev=su1;
};
};
};//loop through seeds
//find max coverage
typeSuperTrSeedCount countMax=0;
//float countOverSuperTrLenMax=0;
for (uint32 ii=0; ii<2*superTrome.N; ii++) {
countMax=max(superTrSeedCount[ii], countMax);
//countOverSuperTrLenMax=max(superTrSeedCount[ii]/float(superTr.length[ii%superTr.N]), countOverSuperTrLenMax);
};
if (countMax<readLen*seedCoverageThreshold/seedSpacing)//no good candidates, hard-coded for now
return;
uint32 nSuperTr=0;
uint32 maxMaxScore=0;
for (uint32 ii=0; ii<superTrome.N; ii++) {//selection cycle
uint32 sutr1=ii%superTrome.N;
uint32 str1=ii/superTrome.N;
//if (superTrSeedCount[ii]<countOverSuperTrLenMax*superTr.length[sutr1]*seedCoverageMinToMax)
//if (superTrSeedCount[ii]<countMax*seedCoverageMinToMax)
if (superTrSeedCount[ii] < readLen*seedCoverageThreshold/seedSpacing || superTrSeedCount[ii]<countMax*seedCoverageMinToMax) {
continue;
};
if (readLen>=100000 || superTrome.superTrs[sutr1].length*readLen>=1000000000) {//temporary restriction: will lift after redoing the scoringMatrix
continue;
};
//convert into trAll
RA->trAll[nSuperTr]=RA->trArrayPointer+nSuperTr;
RA->nWinTr[nSuperTr]=1;
Transcript &trA = *RA->trAll[nSuperTr][0]; //transcript to fill
trA=*RA->trInit;
trA.Chr=sutr1;
trA.Str=str1;
uint32 swScore = 0;
swScore = swScoreSpliced((str1==0 ? readSeq : readSeqRevCompl), readLen, superTrome.superTrs[sutr1], trA.cigar);
//swTraceBack(alignInfo.aEnd, alignInfo.aStart);
//float(superTrSeedCount[ii])/countMax
//float(superTrSeedCount[ii])/superTr.length[sutr1]/countOverSuperTrLenMax <<'\t'<<
cout << readName <<'\t'<< sutr1 <<'\t'<< str1 <<'\t'<< superTrome.superTrs[sutr1].length <<'\t'<< readLen <<'\t'<< float(superTrSeedCount[ii])/readLen*seedSpacing <<'\t'<<
float(superTrSeedCount[ii])/countMax <<'\t'<<
swScore <<'\t'<< float(swScore)/readLen <<'\t'<< alignInfo.aStart[0] <<'\t'<< alignInfo.aEnd[0] <<'\t'<< alignInfo.aStart[1] <<'\t'<< alignInfo.aEnd[1] << endl;
trA.maxScore=swScore;
trA.nMatch=swScore;//TODO fix this, calculate number of matched bases
trA.nExons=0;
trA.gStart=mapGen.chrStart[trA.Chr]+alignInfo.aStart[1];
trA.nMM=alignInfo.nMM;
trA.lIns=alignInfo.nI;
trA.lDel=alignInfo.nD;
trA.rLength=alignInfo.nMap;
// {//calculate blocks from rowCol and rowSJ
// int32 iEx=-1;//current exon
// for (uint32 row=alignInfo.aStart[0]; row<=alignInfo.aEnd[0]; row++) {
//
// if (rowCol[row]>=0) {//this row has no mapped base (i.e. no block) = bases deleted from query
// if (iEx==-1 || rowCol[row]!=rowCol[row-1]+1) {//start new block
// ++iEx;
// trA.exons[iEx][EX_R]=row;
// trA.exons[iEx][EX_G]=mapGen.chrStart[trA.Chr]+rowCol[row];
// trA.exons[iEx][EX_L]=1;
// trA.canonSJ[iEx]=-1;
// trA.sjAnnot[iEx]=0;
// } else {
// trA.exons[iEx][EX_L]++;
// };
// };
//
// //this needs to be done even if rowCol[row]==-1
// if (rowSJ[row][0]>=0) {//junction: create two 0-length blocks to encapsulate junction
// ++iEx;
// trA.exons[iEx][EX_R]=row+1;
// trA.exons[iEx][EX_G]=mapGen.chrStart[trA.Chr]+rowSJ[row][0]+1;
// trA.exons[iEx][EX_L]=0;
// trA.canonSJ[iEx]=1;//TODO actual motif
// trA.sjAnnot[iEx]=1;
// //if (rowSJ[row]!=rowCol[row+1]) {//create 0-length block to mark junction, on the next row
// ++iEx;
// trA.exons[iEx][EX_R]=row+1;
// trA.exons[iEx][EX_G]=mapGen.chrStart[trA.Chr]+rowSJ[row][1];
// trA.exons[iEx][EX_L]=0;
// trA.canonSJ[iEx]=-1;
// trA.sjAnnot[iEx]=0;
// //};
// };
// };
//
// trA.nExons=iEx+1;
//
// for (uint32 iex=0; iex<trA.nExons; iex++) {
// trA.exons[iex][EX_iFrag]=0;
// trA.exons[iex][EX_sjA]=0;
// };
// };
if (swScore>maxMaxScore) {
maxMaxScore=swScore;
RA->trBest=&trA;
};
nSuperTr++;
};
RA->nW=nSuperTr;
return;
};
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