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#include <cmath>
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
#include "stitchAlignToTranscript.h"
#include "extendAlign.h"
#include "binarySearch2.h"
#include "ErrorWarning.h"
void ReadAlign::stitchWindowSeeds (uint iW, uint iWrec, bool *WAexcl, char *R) {//stitches all seeds in one window: iW
for (uint iS1=0;iS1<nWA[iW];iS1++) {
scoreSeedBest[iS1]=0;
scoreSeedBestMM[iS1]=0;
scoreSeedBestInd[iS1]=-1;
if (WAexcl!=NULL && WAexcl[iS1]) continue; //do not include this seed
intScore score2=0;
for (uint iS2=0;iS2<=iS1;iS2++) {
if (WAexcl!=NULL && WAexcl[iS1]) continue; //do not include this seed
trA1=*trInit;//initialize trA1
if (iS2<iS1) {
trA1.nExons=1;
trA1.nMM=scoreSeedBestMM[iS2];
trA1.exons[0][EX_R] = WA[iW][iS2][WA_rStart];
trA1.exons[0][EX_G] = WA[iW][iS2][WA_gStart];
trA1.exons[0][EX_L] = WA[iW][iS2][WA_Length];
trA1.exons[0][EX_iFrag]=WA[iW][iS2][WA_iFrag];
trA1.exons[0][EX_sjA]=WA[iW][iS2][WA_sjA];
score2=\
stitchAlignToTranscript(WA[iW][iS2][WA_rStart]+WA[iW][iS2][WA_Length]-1, WA[iW][iS2][WA_gStart]+WA[iW][iS2][WA_Length]-1,\
WA[iW][iS1][WA_rStart], WA[iW][iS1][WA_gStart], WA[iW][iS1][WA_Length], WA[iW][iS1][WA_iFrag], WA[iW][iS1][WA_sjA], \
P, R, mapGen, &trA1, outFilterMismatchNmaxTotal);
if (P.outFilterBySJoutStage==2 && trA1.nExons>1)
{//junctions have to be present in the filtered set P.sjnovel
uint iex=0;
if (trA1.canonSJ[iex]>=0 && trA1.sjAnnot[iex]==0)
{
uint jS=trA1.exons[iex][EX_G]+trA1.exons[iex][EX_L];
uint jE=trA1.exons[iex+1][EX_G]-1;
if ( binarySearch2(jS,jE,P.sjNovelStart,P.sjNovelEnd,P.sjNovelN) < 0 ) return;
};
};
//check the length of the iS2 exon. TODO: build the transcripts vs iS1, check the actual exon length
bool exonLongEnough = trA1.exons[0][EX_L] >= ( trA1.sjAnnot[0]==0 ? P.alignSJoverhangMin : P.alignSJDBoverhangMin );
if (exonLongEnough && score2>0 && score2+scoreSeedBest[iS2] > scoreSeedBest[iS1] ) {
scoreSeedBest[iS1]=score2+scoreSeedBest[iS2];
scoreSeedBestMM[iS1]=trA1.nMM;
scoreSeedBestInd[iS1]=iS2;
};
} else {//extend to the left
score2=WA[iW][iS1][WA_Length];
if ( WA[iW][iS1][WA_rStart]>0 \
&& extendAlign(R, mapGen.G, WA[iW][iS1][WA_rStart]-1, WA[iW][iS1][WA_gStart]-1, -1, -1, WA[iW][iS1][WA_rStart], 100000, 0, outFilterMismatchNmaxTotal, P.outFilterMismatchNoverLmax, \
P.alignEndsType.ext[WA[iW][iS1][WA_iFrag]][trA.Str], &trA1) ) {//if could extend
score2 += trA1.maxScore;
};
bool exonLongEnough = (WA[iW][iS1][WA_Length]+trA1.extendL) >= P.alignSJoverhangMin; //TODO new parameter to control end exons length
if (exonLongEnough && score2 > scoreSeedBest[iS1] ) {
scoreSeedBest[iS1]=score2;
scoreSeedBestInd[iS1]=iS1;
// scoreSeedBestMM[iS1]=trA1.nMM;
};
};
};
};
intScore scoreBest=0;
uint scoreBestInd=0;
for (uint iS1=0;iS1<nWA[iW];iS1++) {//find the best alignment
trA1=*trInit;//initialize trA1
uint tR2=WA[iW][iS1][WA_rStart]+WA[iW][iS1][WA_Length];
uint tG2=WA[iW][iS1][WA_gStart]+WA[iW][iS1][WA_Length];
if ( tR2 < Lread-1 \
&& extendAlign(R, mapGen.G, tR2, tG2, +1, +1, Lread-tR2, 100000, scoreSeedBestMM[iS1], outFilterMismatchNmaxTotal, P.outFilterMismatchNoverLmax, \
P.alignEndsType.ext[WA[iW][iS1][WA_iFrag]][1-trA.Str], &trA1) )
{//extend to the right
scoreSeedBest[iS1]+=trA1.maxScore;
};
bool exonLongEnough = (WA[iW][iS1][WA_Length]+trA1.extendL) >= P.alignSJoverhangMin; //TODO new parameter to control end exons length
if (exonLongEnough && scoreSeedBest[iS1]>scoreBest) {//record new best transcript
scoreBest=scoreSeedBest[iS1];
scoreBestInd=iS1;
};
};
uint seedN=0;
while (true) {//construct the sequence of seeds
seedChain[seedN++]=scoreBestInd;
WAincl[scoreBestInd]=true;
if (scoreBestInd>scoreSeedBestInd[scoreBestInd]){//keep going
scoreBestInd=scoreSeedBestInd[scoreBestInd];
} else {//this seed is the first one
break;
};
};
int Score=0;
{//build final transcript form seedChain
{//initiate transcript
uint iS1=seedChain[seedN-1];
Score= WA[iW][iS1][WA_Length];
trA.maxScore = Score;
trA.nMatch = WA[iW][iS1][WA_Length]; //# of matches
trA.nMM = 0;
trA.exons[0][EX_R] = trA.rStart = WA[iW][iS1][WA_rStart];
trA.exons[0][EX_G] = trA.gStart = WA[iW][iS1][WA_gStart];
trA.exons[0][EX_L] = WA[iW][iS1][WA_Length];
trA.exons[0][EX_iFrag]=WA[iW][iS1][WA_iFrag];
trA.exons[0][EX_sjA]=WA[iW][iS1][WA_sjA];
trA.nExons=1;
};
for (uint iSc=seedN-1; iSc>0; iSc--) {//stitch seeds from the chain
uint iS1=seedChain[iSc], iS2=seedChain[iSc-1];
int scoreStitch= stitchAlignToTranscript(WA[iW][iS1][WA_rStart]+WA[iW][iS1][WA_Length]-1, WA[iW][iS1][WA_gStart]+WA[iW][iS1][WA_Length]-1,\
WA[iW][iS2][WA_rStart], WA[iW][iS2][WA_gStart], WA[iW][iS2][WA_Length], WA[iW][iS2][WA_iFrag], WA[iW][iS2][WA_sjA], \
P, R, mapGen, &trA, outFilterMismatchNmaxTotal);
// if (scoreStitch>0) {
Score+=scoreStitch;
// } else {
// cout <<"BUG"<<endl;
// return;//this should not happen
// };
};
trA.maxScore=Score;
{//extend to the left
trA1=*trInit;
if ( trA.exons[0][EX_R]>0 \
&& extendAlign(R, mapGen.G, trA.exons[0][EX_R]-1, trA.exons[0][EX_G]-1, -1, -1, trA.exons[0][EX_R], 100000, 0, outFilterMismatchNmaxTotal, P.outFilterMismatchNoverLmax,
P.alignEndsType.ext[trA.exons[0][EX_iFrag]][trA.Str], &trA1) ) {//if could extend
trA.add(&trA1);
trA.exons[0][EX_R] -= trA1.extendL;
trA.exons[0][EX_G] -= trA1.extendL;
trA.exons[0][EX_L] += trA1.extendL;
trA.rStart = trA.exons[0][EX_R];
trA.gStart = trA.exons[0][EX_G];
};
};
{//extend to the right
uint iS1=seedChain[0];
trA1=*trInit;//initialize trA1
uint tR2=WA[iW][iS1][WA_rStart]+WA[iW][iS1][WA_Length];
uint tG2=WA[iW][iS1][WA_gStart]+WA[iW][iS1][WA_Length];
if ( tR2 < Lread \
&& extendAlign(R, mapGen.G, tR2, tG2, +1, +1, Lread-tR2, 100000, scoreSeedBestMM[iS1], outFilterMismatchNmaxTotal, P.outFilterMismatchNoverLmax, \
P.alignEndsType.ext[trA.exons[trA.nExons-1][EX_iFrag]][1-trA.Str], &trA1) ) {//if could extend
trA.add(&trA1);
trA.exons[trA.nExons-1][EX_L] += trA1.extendL;//extend the length of the last exon
};
};
};
//debug: recalculate the number of MM
// {
// uint nMM1=0;
// for (uint iex=0;iex<trA.nExons;iex++) {
// for (uint ii=0;ii<trA.exons[iex][EX_L];ii++) {
// if ( R[ii+trA.exons[iex][EX_R]]!=G[ii+trA.exons[iex][EX_G]] && mapGen.G[ii+trA.exons[iex][EX_G]]<4 && R[ii+trA.exons[iex][EX_R]]<4) {
// nMM1++;
// };
// };
// };
// if (nMM1!=trA.nMM) {
// cout <<nMM1<<" "<<trA.nMM<<" "<<readName<<" "<<iRead<<endl;
// };
// };
{//calculate some final values for the transcript
trA.rLength = 0;
for (uint isj=0;isj<trA.nExons;isj++) {
trA.rLength += trA.exons[isj][EX_L];
};
trA.gLength = trA.exons[trA.nExons-1][EX_G]+1-trA.gStart;
//calculate some final values for the transcript
trA.roStart = (trA.roStr == 0) ? trA.rStart : Lread - trA.rStart - trA.rLength;
if (trA.exons[0][EX_iFrag]==trA.exons[trA.nExons-1][EX_iFrag]) {//mark single fragment transcripts
trA.iFrag=trA.exons[0][EX_iFrag];
maxScoreMate[trA.iFrag] = max (maxScoreMate[trA.iFrag] , trA.maxScore);
} else {
trA.iFrag=-1;
};
if (P.scoreGenomicLengthLog2scale!=0) {//add gap length score
trA.maxScore += int(ceil( log2( (double) ( trA.exons[trA.nExons-1][EX_G]+trA.exons[trA.nExons-1][EX_L] - trA.exons[0][EX_G]) ) \
* P.scoreGenomicLengthLog2scale - 0.5));
trA.maxScore = max(0,trA.maxScore);
};
//filter strand consistency
uint sjN=0;
trA.intronMotifs[0]=0;trA.intronMotifs[1]=0;trA.intronMotifs[2]=0;
for (uint iex=0;iex<trA.nExons-1;iex++) {
if (trA.canonSJ[iex]>=0)
{//junctions - others are indels
sjN++;
trA.intronMotifs[trA.sjStr[iex]]++;
};
};
if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]==0)
trA.sjMotifStrand=1;
else if (trA.intronMotifs[1]==0 && trA.intronMotifs[2]>0)
trA.sjMotifStrand=2;
else
trA.sjMotifStrand=0;
if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]>0 && P.outFilterIntronStrands=="RemoveInconsistentStrands")
return;
if (sjN>0 && trA.sjMotifStrand==0 && P.outSAMstrandField.type==1) {//strand not defined for a junction
return;
};
if (P.outFilterIntronMotifs=="None") {//no filtering
} else if (P.outFilterIntronMotifs=="RemoveNoncanonical") {
for (uint iex=0;iex<trA.nExons-1;iex++) {
if (trA.canonSJ[iex]==0) return;
};
} else if (P.outFilterIntronMotifs=="RemoveNoncanonicalUnannotated") {
for (uint iex=0;iex<trA.nExons-1;iex++) {
if (trA.canonSJ[iex]==0 && trA.sjAnnot[iex]==0) return;
};
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT error: unrecognized value of --outFilterIntronMotifs=" <<P.outFilterIntronMotifs <<"\n";
errOut << "SOLUTION: re-run STAR with --outFilterIntronMotifs = None -OR- RemoveNoncanonical -OR- RemoveNoncanonicalUnannotated\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
// if (P.outFilterIntronMotifs=="KeepCanonical" && (trA.intronMotifs[0]>0 || (trA.intronMotifs[1]>0 && trA.intronMotifs[2]>0) ) ) {//keep only conistent canonical introns
// return;
// };
//check exons lengths including repeats, do not report a transcript with short exons
// for (uint isj=0;isj<trA.nExons-1;isj++) {//check exons for min length, if they precede a junction
// if ( trA.canonSJ[isj]>=0 &&
// ( trA.exons[isj][EX_L] < P.alignSJoverhangMin + trA.shiftSJ[isj][0]
// || trA.exons[isj+1][EX_L] < P.alignSJoverhangMin + trA.shiftSJ[isj][1]) ) {
// return;//do not record this transcript in wTr
// };
// };
};
if (WAexcl==NULL)
{//record the transcript TODO: allow for multiple transcripts in one window
*(trAll[iWrec][0])=trA;
nWinTr[iWrec]=1;
} else
{//record 2nd best alignment in this window
*(trAll[iWrec][1])=trA;
nWinTr[iWrec]=2;
};
};
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