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#include "Transcriptome.h"
#include "ReadAlign.h"
#include "serviceFuns.cpp"
#include "AlignVsTranscript.h"
#include "ReadAnnotations.h"
#include <bitset>
int32 alignBlocksOverlapExons(Transcript &aG, uint16 exN1, uint32 *exSE1, uint64 trStart1, bool &sjConcord);
void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandType, ReadAnnotFeature &annFeat)
{
struct GeneStrOverlapAlign {
uint32 g;
int32 ov;
uint32 ia;
uint32 exl;
bool str;
bool sjc;
};
//vector<GeneStrOverlapAlign> vGeStrOvAl;
//vGeStrOvAl.reserve(256); //TODO: check if this affects speed
typedef array<bool,6> OverlapTypes;
struct GeneInfo1 {
uint32 g;
uint32 ia;
OverlapTypes ot; //overlap types, prioritized
};
vector<GeneInfo1> vGeneInfo1;
vGeneInfo1.reserve(256); //TODO: check if this affects speed
OverlapTypes otAS={false,true,false,true,false,true}; //which OverlapTypes is antisense, it will not be counted
/*//GeneFullClosest3p
uint64 minDist3p=(uint64)-1;
uint32 minDist3pGene=(uint32)-1;
*/
for (uint32 iag=0; iag<nA; iag++) {
Transcript &aG=*aAll[iag];
//TODO: this only works if PE mates do not protrude. It's better to find the min-start max-end genomic coordinates for all exons.
uint64 aGstart=aG.exons[0][EX_G];
uint64 aGend=aG.exons[aG.nExons-1][EX_G]+aG.exons[aG.nExons-1][EX_L]-1;
//binary search through transcript starts
uint32 tr1=binarySearch1a<uint>(aGstart, trS, nTr);//tr1 has the maximum transcript start such that it is still <= align start: aGstart>=trS[tr1]
if (tr1==(uint32) -1)
continue; //this alignment is outside of range of all transcripts
++tr1;
do {//cycle back through all the transcripts
--tr1;
if ( aGend>trE[tr1] ) //alignment end is outside of this transcript
continue;
bool str1 = int(strandType==0 ? aG.Str : 1-aG.Str) == (trStr[tr1]-1);
str1 = str1 || (strandType==-1);
/*
//GeneFullClosest3p
if ( str1 ) {
uint64 dist3p = ( aG.Str==0 ? trE[tr1]-aGend : aGstart-trS[tr1] );
if ( dist3p < minDist3p ) {
minDist3p = dist3p;
minDist3pGene = trGene[tr1];
continue;
};
};
*/
bool sjConcord;
int32 nOverlap = alignBlocksOverlapExons(aG, trExN[tr1], exSE+2*trExI[tr1], trS[tr1], sjConcord);
if ( nOverlap>=0 ) {
int exl=0;
for (uint64 iex=0; iex<aG.nExons;iex++)
exl += aG.exons[iex][EX_L];
//vGeStrOvAl.push_back({trGene[tr1], nOverlap, iag, exl, str1, sjConcord});
vGeneInfo1.push_back({trGene[tr1], iag, {
str1 && nOverlap==exl && sjConcord,
!str1 && nOverlap==exl && sjConcord,
str1 && nOverlap>exl/2,
!str1 && nOverlap>exl/2,
str1,
!str1
}
});
/* matches Gene
vGeneInfo1.push_back({trGene[tr1], iag, {
str1 && nOverlap==exl && sjConcord,
false,
false,
false
}
});
*/
/* matches GeneFull_ExonOverIntron
vGeneInfo1.push_back({trGene[tr1], iag, {
str1 && nOverlap==exl && sjConcord,
false,
false,
str1
}
});
*/
/*
bool sjann=true;
for (uint64 iex=0; iex<aG.nExons-1;iex++)
sjann = sjann & (aG.canonSJ[iex]<0 || aG.sjAnnot[iex]!=0);
if ( str1 && nOverlap==exl && sjConcord ) {//this should match geneConcordant
annFeat.fSet.insert(trGene[tr1]);
};
*/
};
//cout << trGene[tr1] <<" "<< nOverlap << " " <<flush;
} while (trEmax[tr1]>=aGend && tr1>0);
};
/*
{//GeneFullClosest3p
annFeat.fSet={};
annFeat.fAlign = {};
annFeat.fAlign.resize(nA);
if (nA==1 && minDist3pGene!=(uint32)-1) {
annFeat.fSet.insert(minDist3pGene);
annFeat.fAlign[0].insert(minDist3pGene);
};
return;
};
*/
{//prune geneFull_Ex50pAS according to priorities
/*
bool bTranscr = false; //transcriptomic
bool bExonic = false; //sense, exonic: >=50% exonic
bool bExonicAS = false;
bool bIntronic = false; //sense, intronic
for (auto &v1: vGeStrOvAl) {
if ( v1.str ) {//sense
if (v1.ov==v1.exl && v1.sjc) {
bTranscr = true;
break; //this is the highest priority
} else if (v1.ov>=v1.exl/2) {
bExonic = true;
} else {
bIntronic = true;
};
} else if (v1.ov>=v1.exl/2) {
bExonicAS = true;
};
};
for (auto &v1: vGeneInfo1) {
if ( v1.tr ) {//sense
bTranscr = true;
break; //this is the highest priority
} else if ( v1.ex ) {
bExonic = true;
} else if ( v1.as ) {
bExonicAS = true;
} else if (v1.in) {
bIntronic = true;
};
};
if (bTranscr) {
for (auto &v1: vGeneInfo1)
if ( v1.tr )
annFeat.fSet.insert(v1.g);
} else if (bExonic) {
for (auto &v1: vGeneInfo1)
if ( v1.ex )
annFeat.fSet.insert(v1.g);
} else if (bIntronic) {
for (auto &v1: vGeneInfo1)
if ( v1.in )
annFeat.fSet.insert(v1.g);
};
*/
OverlapTypes otFinal={};
for ( auto &v1: vGeneInfo1 ) {
for ( uint32 it=0; it<otFinal.size(); it++ ) {
if ( v1.ot[it] ) {
otFinal[it] = true;
break; //lower it are prioritized over higher
};
};
};
if (otFinal[0]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::exonic;
} else if (otFinal[1]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::exonicAS;
} else if (otFinal[2]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::exonic50p;
} else if (otFinal[3]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::exonic50pAS;
} else if (otFinal[4]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::intronic;
} else if (otFinal[5]) {
annFeat.ovType = ReadAnnotFeature::overlapTypes::intronicAS;
} else {
annFeat.ovType = ReadAnnotFeature::overlapTypes::intergenic; //intergenic. i.e. no overlap with genes
};
// annFeat.fSet={};
// annFeat.fAlign = {};
annFeat.fAlign.resize(nA);
for ( uint32 it=0; it<otFinal.size(); it++ ) {
if ( otFinal[it] ) {
if (otAS[it])
return; //AS reads are not counted TODO: add to stats
for ( auto &v1: vGeneInfo1 ) {
if ( v1.ot[it] ) {
annFeat.fSet.insert(v1.g);
annFeat.fAlign[v1.ia].insert(v1.g);
};
};
break;//first otFinal wins
};
};
};
};
int32 alignBlocksOverlapExons(Transcript &aG, uint16 exN1, uint32 *exSE1, uint64 trStart1, bool &sjConcord)
{//calculate overlap between blocks of align and transcript
uint32 i1=0, i2=0;
int32 nOverlap = 0;
sjConcord = true;
//trStart1 += exSE1[0]; //not really needed since exSE1[0]=0
uint64 trEnd1 = trStart1 + exSE1[2*exN1-1] + 1;//1st base after the end
while (i1<aG.nExons && i2<exN1) {//scan through all blocks and exons
uint64 rs1 = aG.exons[i1][EX_G];
uint64 re1 = aG.exons[i1][EX_G]+aG.exons[i1][EX_L];//1st base after the end
uint64 rs2 = trStart1 + exSE1[2*i2];
uint64 re2 = trStart1 + exSE1[2*i2+1] + 1;
if (rs1 < trStart1 || re1 > trEnd1) //this can happen for PE reads, when the 2nd mate protrudes to the left of the first or vice versa
return -1;
if (rs1>=re2) {//t1 block is on the right to t2, no hope of overlap
i2++;
if (i1>0 && aG.canonSJ[i1-1]>=0)
sjConcord = false; //only 1st align block does not have to match exon start
} else if (rs2>=re1) {//t2 block is on the right to t1, no hope of overlap
i1++;
sjConcord = false;
} else {//overlap
nOverlap += min(re1,re2) - max(rs1,rs2);
if (i1>0 && rs1!=rs2 && aG.canonSJ[i1-1]>=0 )
sjConcord = false;
if (i1<aG.nExons-1 && re1!=re2 && aG.canonSJ[i1]>=0 )
sjConcord = false;
if (re1>=re2)
i2++;//1 is on the right of 2
if (re2>=re1)
i1++;//2 is on the right of 1
};
};
return nOverlap;
};
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