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#include "sjdbPrepare.h"
#include "ErrorWarning.h"
#include "serviceFuns.cpp"
void sjdbPrepare (SjdbClass &sjdbLoci, Parameters &P, uint nGenomeReal, string outDir, Genome &mapGen, char *Gsj) {
char *G=mapGen.G;
uint *sjdbS=new uint [sjdbLoci.chr.size()];
uint *sjdbE=new uint [sjdbLoci.chr.size()];
uint8 *sjdbMotif=new uint8 [sjdbLoci.chr.size()];
uint8 *sjdbShiftLeft=new uint8 [sjdbLoci.chr.size()];
uint8 *sjdbShiftRight=new uint8 [sjdbLoci.chr.size()];
string chrOld="";
uint iChr=0;
for (uint ii=0;ii<sjdbLoci.chr.size();ii++) {
if (chrOld!=sjdbLoci.chr.at(ii)) {//find numeric value of the chr
for (iChr=0;iChr<mapGen.nChrReal;iChr++) {
if (sjdbLoci.chr.at(ii)==mapGen.chrName[iChr]) break;
};
if (iChr>=mapGen.nChrReal) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, the sjdb chromosome " << sjdbLoci.chr.at(ii) << " is not found among the genomic chromosomes\n";
errOut << "SOLUTION: fix your file(s) --sjdbFileChrStartEnd or --sjdbGTFfile, offending junction:" <<sjdbLoci.chr.at(ii)<<"\t"<<sjdbLoci.start.at(ii)<<"\t"<<sjdbLoci.end.at(ii)<<"\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
chrOld=sjdbLoci.chr.at(ii);
};
sjdbS[ii] = sjdbLoci.start.at(ii) + mapGen.chrStart[iChr] - 1;//sj names contain 1-based intron loci
sjdbE[ii] = sjdbLoci.end.at(ii) + mapGen.chrStart[iChr] - 1;
//motifs
if ( G[sjdbS[ii]]==2 && G[sjdbS[ii]+1]==3 && G[sjdbE[ii]-1]==0 && G[sjdbE[ii]]==2 ) {//GTAG
sjdbMotif[ii]=1;
} else if ( G[sjdbS[ii]]==1 && G[sjdbS[ii]+1]==3 && G[sjdbE[ii]-1]==0 && G[sjdbE[ii]]==1 ) {//CTAC
sjdbMotif[ii]=2;
} else if ( G[sjdbS[ii]]==2 && G[sjdbS[ii]+1]==1 && G[sjdbE[ii]-1]==0 && G[sjdbE[ii]]==2 ) {//GCAG
sjdbMotif[ii]=3;
} else if ( G[sjdbS[ii]]==1 && G[sjdbS[ii]+1]==3 && G[sjdbE[ii]-1]==2 && G[sjdbE[ii]]==1 ) {//CTGC
sjdbMotif[ii]=4;
} else if ( G[sjdbS[ii]]==0 && G[sjdbS[ii]+1]==3 && G[sjdbE[ii]-1]==0 && G[sjdbE[ii]]==1 ) {//ATAC
sjdbMotif[ii]=5;
} else if ( G[sjdbS[ii]]==2 && G[sjdbS[ii]+1]==3 && G[sjdbE[ii]-1]==0 && G[sjdbE[ii]]==3 ) {//GTAT
sjdbMotif[ii]=6;
} else {
sjdbMotif[ii]=0;
};
//repeat length: go back and forth around jR to find repeat length
uint jjL=0,jjR=0;
while ( jjL <= sjdbS[ii]-1 && G[sjdbS[ii]-1-jjL]==G[sjdbE[ii]-jjL] && G[sjdbS[ii]-1-jjL]<4 && jjL<255) {//go back
jjL++;
};
sjdbShiftLeft[ii]=jjL;
while ( sjdbS[ii]+jjR < nGenomeReal && G[sjdbS[ii]+jjR]==G[sjdbE[ii]+1+jjR] && G[sjdbS[ii]+jjR]<4 && jjR<255) {//go forward
jjR++;
};
sjdbShiftRight[ii]=jjR;
if (jjR==255 || jjL==255) {
P.inOut->logMain << "WARNING: long repeat for junction # " << ii+1 <<" : " \
<< sjdbLoci.chr.at(ii) <<" "<<sjdbS[ii] - mapGen.chrStart[iChr] + 1 <<" "<< sjdbE[ii] - mapGen.chrStart[iChr] + 1 \
<< "; left shift = "<< (int) sjdbShiftLeft[ii] <<"; right shift = "<< (int) sjdbShiftRight[ii] <<"\n";
};
sjdbS[ii]-=sjdbShiftLeft[ii];
sjdbE[ii]-=sjdbShiftLeft[ii];
};
//sort sjdb
uint *sjdbSort=new uint [sjdbLoci.chr.size()*3];
for (uint ii=0;ii<sjdbLoci.chr.size();ii++) {
uint shift1=0;
switch (sjdbLoci.str.at(ii)) {
case '+':
shift1=0;
break;
case '-':
shift1=nGenomeReal;
break;
default:
shift1=2*nGenomeReal;
};
sjdbSort[ii*3]=sjdbS[ii]+shift1; //separate sorting of +/- strand
sjdbSort[ii*3+1]=sjdbE[ii]+shift1;
sjdbSort[ii*3+2]=ii;
};
qsort((void *) sjdbSort, sjdbLoci.chr.size(), sizeof(uint)*3, funCompareUint2);
uint *I=new uint [sjdbLoci.chr.size()];
uint nsj=0;
for (uint ii=0;ii<sjdbLoci.chr.size();ii++) {
uint isj=sjdbSort[ii*3+2];//index of the next sorted junction
uint isj0;
if (nsj>0)
{
isj0=I[nsj-1]; //index of the last recorded junctions
};
if (nsj==0 || sjdbS[isj]!=sjdbS[isj0] || sjdbE[isj]!=sjdbE[isj0])
{//different intron coordinates
I[nsj++]=isj;// add new junction
} else if (sjdbLoci.priority.at(isj)<sjdbLoci.priority.at(isj0))
{//new junction has lower priority
//do nothing, i.e. keep the old junction
} else if (sjdbLoci.priority.at(isj)>sjdbLoci.priority.at(isj0))
{//new junction has higher priority
I[nsj-1]=isj;//replace the old junction
} else if ( (sjdbMotif[isj]>0 && sjdbMotif[isj0]==0) \
|| ( ((sjdbMotif[isj]>0) == (sjdbMotif[isj0]>0)) && sjdbShiftLeft[isj]<sjdbShiftLeft[isj0]) ) {
//new and old junctions have the same priority
//new junction is canonical or left-most, so it wins
I[nsj-1]=isj;//replace the old junction
// else - keep the old junction, do not add the new one
};
};
//sort again, after returning canonical junctions back to original loci:
for (uint ii=0;ii<nsj;ii++) {
sjdbSort[ii*3] =sjdbS[I[ii]] + (sjdbMotif[I[ii]]==0 ? 0 : sjdbShiftLeft[I[ii]]);
sjdbSort[ii*3+1]=sjdbE[I[ii]] + (sjdbMotif[I[ii]]==0 ? 0 : sjdbShiftLeft[I[ii]]);
sjdbSort[ii*3+2]=I[ii];
};
qsort((void *) sjdbSort, nsj, sizeof(uint)*3, funCompareUint2);
mapGen.sjdbStart=new uint [nsj];
mapGen.sjdbEnd=new uint [nsj];
mapGen.sjdbMotif=new uint8 [nsj];
mapGen.sjdbShiftLeft=new uint8 [nsj];
mapGen.sjdbShiftRight=new uint8 [nsj];
mapGen.sjdbStrand=new uint8 [nsj];
uint nsj1=0;
for (uint ii=0;ii<nsj;ii++) {
uint isj=sjdbSort[ii*3+2];
if ( nsj1>0 && mapGen.sjdbStart[nsj1-1]==sjdbSort[ii*3] && mapGen.sjdbEnd[nsj1-1]==sjdbSort[ii*3+1] ) {//same loci on opposite strands
uint isj0=sjdbSort[(ii-1)*3+2];
if (sjdbLoci.priority.at(isj)<sjdbLoci.priority.at(isj0))
{//new junction has lower priority
continue;//keep old junction, do not add new
} else if (sjdbLoci.priority.at(isj)>sjdbLoci.priority.at(isj0))
{//new junction has higher priority
nsj1--;//replace the old junction with the new one
} else if (mapGen.sjdbStrand[nsj1-1]>0 && sjdbLoci.str.at(isj)=='.')
{//new junction strand is not defined
continue;
} else if (mapGen.sjdbStrand[nsj1-1]==0 && sjdbLoci.str.at(isj)!='.')
{//old junction strand is not defined
nsj1--; //replace old with new
} else if (mapGen.sjdbMotif[nsj1-1]==0 && sjdbMotif[isj]==0)
{//both are non-canonical (on opposite strand)
mapGen.sjdbStrand[nsj1-1]=0;//do not record new junction, keep old with undefined strand
continue;
} else if ( (mapGen.sjdbMotif[nsj1-1]>0 && sjdbMotif[isj]==0) ||(mapGen.sjdbMotif[nsj1-1]%2 == (2-mapGen.sjdbStrand[nsj1-1])) ){//both strands defined, both junctions canonical
//old junction is canonical, new is not, OR old junction is on correct strand
continue;
} else {
//new junction is on correct strand, replace the old one
nsj1--;
};
};
//record junction
mapGen.sjdbStart[nsj1]=sjdbSort[ii*3];
mapGen.sjdbEnd[nsj1]=sjdbSort[ii*3+1];
mapGen.sjdbMotif[nsj1]=sjdbMotif[isj];
mapGen.sjdbShiftLeft[nsj1]=sjdbShiftLeft[isj];
mapGen.sjdbShiftRight[nsj1]=sjdbShiftRight[isj];
if (sjdbLoci.str.at(isj)=='+') {
mapGen.sjdbStrand[nsj1]=1;
} else if (sjdbLoci.str.at(isj)=='-') {
mapGen.sjdbStrand[nsj1]=2;
} else {
if (mapGen.sjdbMotif[nsj1]==0) {//strand un-defined
mapGen.sjdbStrand[nsj1]=0;
} else {
mapGen.sjdbStrand[nsj1]=2-mapGen.sjdbMotif[nsj1]%2;
};
};
nsj1++;
};
mapGen.sjdbN=nsj1;
mapGen.sjDstart = new uint [mapGen.sjdbN];
mapGen.sjAstart = new uint [mapGen.sjdbN];
ofstream sjdbInfo((outDir+"/sjdbInfo.txt").c_str());
ofstream sjdbList ((outDir+"/sjdbList.out.tab").c_str());
char strandChar[3]={'.','+','-'};
//first line is some general useful information
sjdbInfo << mapGen.sjdbN <<"\t"<< mapGen.sjdbOverhang <<"\n";
uint sjGstart=0;
for (uint ii=0;ii<mapGen.sjdbN;ii++)
{//add sjdb sequence to genome
mapGen.sjDstart[ii] = mapGen.sjdbStart[ii] - mapGen.sjdbOverhang;
mapGen.sjAstart[ii] = mapGen.sjdbEnd[ii] + 1;
if (mapGen.sjdbMotif[ii]==0) {//shift non-canonical junctions back to their true coordinates
mapGen.sjDstart[ii] += mapGen.sjdbShiftLeft[ii];
mapGen.sjAstart[ii] += mapGen.sjdbShiftLeft[ii];
};
memcpy(Gsj+sjGstart,G+mapGen.sjDstart[ii],mapGen.sjdbOverhang);//sjdbStart contains 1-based intron loci
memcpy(Gsj+sjGstart+mapGen.sjdbOverhang,G+mapGen.sjAstart[ii],mapGen.sjdbOverhang);//sjdbStart contains 1-based intron loci
sjGstart += mapGen.sjdbLength;
Gsj[sjGstart-1]=GENOME_spacingChar;//spacing char between the sjdb seqs
sjdbInfo << mapGen.sjdbStart[ii] <<"\t"<< mapGen.sjdbEnd[ii] <<"\t"<<(int) mapGen.sjdbMotif[ii] <<"\t"<<(int) mapGen.sjdbShiftLeft[ii] <<"\t"<<(int) mapGen.sjdbShiftRight[ii]<<"\t"<<(int) mapGen.sjdbStrand[ii] <<"\n";
uint chr1=mapGen.chrBin[ mapGen.sjdbStart[ii] >> P.pGe.gChrBinNbits];
sjdbList << mapGen.chrName[chr1]<< "\t" << mapGen.sjdbStart[ii]-mapGen.chrStart[chr1] + 1 + (mapGen.sjdbMotif[ii]>0 ? 0:mapGen.sjdbShiftLeft[ii]) \
<< "\t"<< mapGen.sjdbEnd[ii]-mapGen.chrStart[chr1] + 1 + (mapGen.sjdbMotif[ii]>0 ? 0:mapGen.sjdbShiftLeft[ii]) \
<< "\t"<< strandChar[mapGen.sjdbStrand[ii]]<<"\n";
};
sjdbInfo.close();
sjdbList.close();
};
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