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#include "Transcript.h"
#include "binarySearch2.h"
bool Transcript::transformGenome(Genome &genOut, Transcript & A)
{
uint32 nB=0;//number of out blocks
auto &coBl=genOut.genomeOut.convBlocks;
//uint64 icb=0;
//auto cBit=coBl.begin();
for (uint32 iA=0; iA<nExons; iA++) {//loop over blocks
uint64 r1=exons[iA][EX_R];//r start of a-block
uint64 len=exons[iA][EX_L];
uint64 g1=exons[iA][EX_G];//g start of a-block
uint64 g2=g1+len-1;//end of a-block
//find c-block whose start is on the left of a-block
array<uint64,3> g1array = {g1,0,0};
auto cBit=coBl.begin(); //TODO might reuse previous value of cBit, but need to take care of overlapping mates
cBit = std::upper_bound(cBit, coBl.end(), g1array,
[](const array<uint64,3> &t1, const array<uint64,3> &t2)
{
return t1[0] < t2[0];
});
--cBit;//upperbound finds element > value, need to step back
//icb=binarySearchStride(coBl.data(), coBl.size(), exons[iA][EX_G], icb, 3);
uint64 b1=(*cBit)[0];
uint64 b2=(*cBit)[0]+(*cBit)[1]-1;
uint64 b1o=(*cBit)[2];
/* **********---********----********
* b1 b2
* ++++++++++++++++
* g1 g2
*/
if (g1 <= b2 ) {//fill the first o-block
A.exons[nB][EX_iFrag]=exons[iA][EX_iFrag];
A.exons[nB][EX_R] = r1;
A.exons[nB][EX_G] = b1o + g1 - b1;
if (g2<=b2) {//g2 inside this c-block
A.exons[nB][EX_L]=len;
} else {//g2 is past the end of this c-block
A.exons[nB][EX_L]=b2-g1+1;
};
++nB;
};
++cBit;
while (g2 >= (*cBit)[0]) {//until c-block start is to the right of g2
A.exons[nB][EX_iFrag]=exons[iA][EX_iFrag];
A.exons[nB][EX_G]=(*cBit)[2];
A.exons[nB][EX_R]=r1+(*cBit)[0]-g1;
if (g2 < (*cBit)[0]+(*cBit)[1]) {//g2 inside this c-block
A.exons[nB][EX_L]=g2-(*cBit)[0]+1;
} else {//g2 is past the end of this c-block
A.exons[nB][EX_L]=(*cBit)[1];//full block length
};
++nB;
++cBit;
};
--cBit;
};
if (nB==0)
return false; //transformation did not work
{//merge exons w/o R/G gaps
uint32 nB1 = 1;
for ( uint32 ib=1; ib<nB; ib++) {
if (nB1!=ib) {//copy ib into nB1
for (uint32 ii=0; ii<EX_SIZE; ii++)
A.exons[nB1][ii] = A.exons[ib][ii];
};
if (A.exons[nB1][EX_iFrag]!=A.exons[nB1-1][EX_iFrag]) {//gap between mates, do not adjust
++nB1;
continue;
};
uint64 gapR = A.exons[nB1][EX_R] - A.exons[nB1-1][EX_R] - A.exons[nB1-1][EX_L];
uint64 gapG = A.exons[nB1][EX_G] - A.exons[nB1-1][EX_G] - A.exons[nB1-1][EX_L];
if ( gapR == gapG) {//eliminate both gaps by increasing previous exon length
A.exons[nB1-1][EX_L] += A.exons[nB1][EX_L] + gapR;
} else {//new exon
uint64 minGap = min(gapR, gapG);
if (minGap>0) {//flush the gap to the left
A.exons[nB1][EX_L] += minGap;
A.exons[nB1][EX_G] -= minGap;
A.exons[nB1][EX_R] -= minGap;
};
++nB1;
};
};
nB = nB1;
};
A.nExons=nB;
A.Str = Str;
A.Chr = genOut.chrBin[A.exons[0][EX_G] >> genOut.pGe.gChrBinNbits];
{//recalculate canonSJ, sjAnnot
for (uint64 ia=0; ia<A.nExons-1; ia++) {
A.sjAnnot[ia]=0;
if (A.exons[ia+1][EX_iFrag]!=A.exons[ia][EX_iFrag]) {//mate gap
A.canonSJ[ia]=-3;
continue;
};
uint64 jS=A.exons[ia][EX_G]+A.exons[ia][EX_L];
uint64 jE=A.exons[ia+1][EX_G]-1;//intron start/end
int sjdbInd=binarySearch2(jS, jE, genOut.sjdbStart, genOut.sjdbEnd, genOut.sjdbN);
if (sjdbInd>=0) {//annotated
A.sjAnnot[ia] = 1;
A.canonSJ[ia] = genOut.sjdbMotif[sjdbInd];
if (genOut.sjdbMotif[sjdbInd]==0) {//shift to match annotations
if (A.exons[ia][EX_L] <= genOut.sjdbShiftLeft[sjdbInd]) {
return false; //this align is not allowed
};
A.exons[ia][EX_L] -= genOut.sjdbShiftLeft[sjdbInd];
A.exons[ia+1][EX_G] -= genOut.sjdbShiftLeft[sjdbInd];
};
} else {//unannotated
uint64 gapG=jE-jS+1;
uint64 gapR=A.exons[ia+1][EX_R]-A.exons[ia][EX_R]-A.exons[ia][EX_L];
if (gapR>0) {//insertion
A.canonSJ[ia]=-2;
} else if (gapG>=genOut.P.alignIntronMin) {//junction
A.canonSJ[ia]=0;
if ( genOut.G[jS]==2 && genOut.G[jS+1]==3 && genOut.G[jE-1]==0 && genOut.G[jE]==2 ) {//GTAG
A.canonSJ[ia]=1;
} else if ( genOut.G[jS]==1 && genOut.G[jS+1]==3 && genOut.G[jE-1]==0 && genOut.G[jE]==1 ) {//CTAC
A.canonSJ[ia]=2;
} else if ( genOut.G[jS]==2 && genOut.G[jS+1]==1 && genOut.G[jE-1]==0 && genOut.G[jE]==2 ) {//GCAG
A.canonSJ[ia]=3;
} else if ( genOut.G[jS]==1 && genOut.G[jS+1]==3 && genOut.G[jE-1]==2 && genOut.G[jE]==1 ) {//CTGC
A.canonSJ[ia]=4;
} else if ( genOut.G[jS]==0 && genOut.G[jS+1]==3 && genOut.G[jE-1]==0 && genOut.G[jE]==1 ) {//ATAC
A.canonSJ[ia]=5;
} else if ( genOut.G[jS]==2 && genOut.G[jS+1]==3 && genOut.G[jE-1]==0 && genOut.G[jE]==3 ) {//GTAT
A.canonSJ[ia]=6;
};
} else {//deletion
A.canonSJ[ia]=-1;
};
};
};
};
return true;
};
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