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/*
* inserts sequences into the SA
* returns number of SA indexes inserted
*/
#include "insertSeqSA.h"
#include "ErrorWarning.h"
#include "SuffixArrayFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"
#include "streamFuns.h"
#include "binarySearch2.h"
#include "funCompareUintAndSuffixes.h"
#include "funCompareUintAndSuffixesMemcmp.h"
#include <cmath>
#include "genomeSAindex.h"
#include "sortSuffixesBucket.h"
uint insertSeqSA(PackedArray & SA, PackedArray & SA1, PackedArray & SAi, char * G, char * G1, uint64 nG, uint64 nG1, uint64 nG2, Parameters & P, Genome &mapGen)
{//insert new sequences into the SA
uint GstrandBit1 = (uint) floor(log(nG+nG1)/log(2))+1;
if (GstrandBit1<32) GstrandBit1=32; //TODO: use simple access function for SA
if ( GstrandBit1+1 != SA.wordLength)
{//sequence is too long - GstrandBit changed
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem\n";
errOut << "SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_GENOME_FILES, P);
};
uint N2bit= 1LLU << (SA.wordLength-1);
uint strandMask=~N2bit;
for (uint64 isa=0;isa<SA.length; isa++)
{
uint64 ind1=SA[isa];
if ( (ind1 & N2bit)>0 )
{//- strand
if ( (ind1 & strandMask)>=nG2 )
{//the first nG bases
ind1+=nG1; //reverse complementary indices are all shifted by the length of the sequence
SA.writePacked(isa,ind1);
};
} else
{//+ strand
if ( ind1>=nG )
{//the last nG2 bases
ind1+=nG1; //reverse complementary indices are all shifted by the length of the sequence
SA.writePacked(isa,ind1);
};
};
};
char** seq1=new char*[2];
#define GENOME_endFillL 16
char* seqq=new char [4*nG1+3*GENOME_endFillL];//ends shouldbe filled with 5 to mark boundaries
seq1[0]=seqq+GENOME_endFillL;//TODO: avoid defining an extra array, use reverse search
seq1[1]=seqq+2*GENOME_endFillL+2*nG1;
memset(seqq,GENOME_spacingChar,GENOME_endFillL);
memset(seqq+2*nG1+GENOME_endFillL,GENOME_spacingChar,GENOME_endFillL);
memset(seqq+4*nG1+2*GENOME_endFillL,GENOME_spacingChar,GENOME_endFillL);
memcpy(seq1[0], G1, nG1);
for (uint ii=0; ii<nG1; ii++)
{//reverse complement sequence
seq1[0][2*nG1-1-ii]=seq1[0][ii]<4 ? 3-seq1[0][ii] : seq1[0][ii];
};
complementSeqNumbers(seq1[0], seq1[1], 2*nG1);//complement
uint64* indArray=new uint64[nG1*2*2+2];// for each base, 1st number - insertion place in SA, 2nd number - index, *2 for reverse compl
#pragma omp parallel num_threads(P.runThreadN)
#pragma omp for schedule (dynamic,1000)
for (uint ii=0; ii<2*nG1; ii++) {//find insertion points for each of the sequences
if (seq1[0][ii]>3)
{//no index for suffices starting with N
indArray[ii*2]=-1;
} else
{
indArray[ii*2] = suffixArraySearch1(mapGen, seq1, ii, 10000, nG, (ii<nG1 ? true:false), 0, SA.length-1, 0) ;
indArray[ii*2+1] = ii;
};
};
uint64 nInd=0;//true number of new indices
for (uint ii=0; ii<2*nG1; ii++) {//remove entries that cannot be inserted, this cannot be done in the parallel cycle above
if (indArray[ii*2]!= (uint) -1) {
indArray[nInd*2]=indArray[ii*2];
indArray[nInd*2+1]=indArray[ii*2+1];
++nInd;
};
};
time_t rawtime;
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished SA search, number of new SA indices = "<<nInd<<endl;
/*//old-debug
uint64* indArray1=new uint64[nG1*2*2+2];
memcpy((void*) indArray1, (void*) indArray, 8*(nG1*2*2+2));
g_funCompareUintAndSuffixes_G=seq1[0];
qsort((void*) indArray1, nInd, 2*sizeof(uint64), funCompareUintAndSuffixes);
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished qsort - old " <<endl;
*/
g_funCompareUintAndSuffixesMemcmp_G=seq1[0];
g_funCompareUintAndSuffixesMemcmp_L=mapGen.pGe.gSuffixLengthMax/sizeof(uint64_t);
qsort((void*) indArray, nInd, 2*sizeof(uint64_t), funCompareUintAndSuffixesMemcmp);
// qsort((void*) indArray, nInd, 2*sizeof(uint64), funCompareUint2);
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished qsort" <<endl;
/*//new sorting, 2-step: qsort for indArray, bucket sort for suffixes
qsort((void*) indArray, nInd, 2*sizeof(uint64), funCompareUint2);
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished qsort"<<nInd<<endl;
sortSuffixesBucket(seq1[0], (void*) indArray, nInd, 2*sizeof(uint64));
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished ordering suffixes"<<nInd<<endl;
*/
/* //debug
for (int ii=0;ii<2*nInd;ii++)
{
if (indArray[ii]!=indArray1[ii])
{
cout << ii <<" "<< indArray[ii] <<" "<< indArray1[ii] <<endl;
};
};
*/
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished sorting SA indices"<<endl;
indArray[2*nInd]=-999; //mark the last junction
indArray[2*nInd+1]=-999; //mark the last junction
SA1.defineBits(SA.wordLength,SA.length+nInd);
/*testing
PackedArray SAo;
SAo.defineBits(mapGen.GstrandBit+1,mapGen.nSA+nInd);
SAo.allocateArray();
ifstream oldSAin("./DirTrue/SA");
oldSAin.read(SAo.charArray,SAo.lengthByte);
oldSAin.close();
*/
uint isa1=0, isa2=0;
for (uint isa=0;isa<SA.length;isa++) {
while (isa==indArray[isa1*2]) {//insert new index before the existing index
uint ind1=indArray[isa1*2+1];
if (ind1<nG1) {
ind1+=nG;
} else {//reverse strand
ind1=(ind1-nG1+nG2) | N2bit;
};
SA1.writePacked(isa2,ind1);
/*testing
if (SA1[isa2]!=SAo[isa2]) {
cout <<isa2 <<" "<< SA1[isa2]<<" "<<SAo[isa2]<<endl;
//sleep(100);
};
*/
++isa2; ++isa1;
};
SA1.writePacked(isa2,SA[isa]); //TODO make sure that the first sj index is not before the first array index
/*testing
if (SA1[isa2]!=SAo[isa2]) {
cout <<isa2 <<" "<< SA1[isa2]<<" "<<SAo[isa2]<<endl;
//sleep(100);
};
*/
++isa2;
};
for (;isa1<nInd;isa1++)
{//insert the last indices
uint ind1=indArray[isa1*2+1];
if (ind1<nG1)
{
ind1+=nG;
} else
{//reverse strand
ind1=(ind1-nG1+nG2) | N2bit;
};
SA1.writePacked(isa2,ind1);
++isa2;
};
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished inserting SA indices" <<endl;
// //SAi insertions
// for (uint iL=0; iL < P.mapGen.gSAindexNbases; iL++) {
// uint iSeq=0;
// uint ind0=mapGen.genomeSAindexStart[iL]-1;//last index that was present in the old genome
// for (uint ii=mapGen.genomeSAindexStart[iL];ii<mapGen.genomeSAindexStart[iL+1]; ii++) {//scan through the longest index
// if (ii==798466)
// cout <<ii;
//
// uint iSA1=SAi[ii];
// uint iSA2=iSA1 & mapGen.SAiMarkNmask & mapGen.SAiMarkAbsentMask;
//
// if ( iSeq<nInd && (iSA1 & mapGen.SAiMarkAbsentMaskC)>0 )
// {//index missing from the old genome
// uint iSeq1=iSeq;
// int64 ind1=funCalcSAi(seq1[0]+indArray[2*iSeq+1],iL);
// while (ind1 < (int64)(ii-mapGen.genomeSAindexStart[iL]) && indArray[2*iSeq]<iSA2) {
// ++iSeq;
// ind1=funCalcSAi(seq1[0]+indArray[2*iSeq+1],iL);
// };
// if (ind1 == (int64)(ii-mapGen.genomeSAindexStart[iL]) ) {
// SAi.writePacked(ii,indArray[2*iSeq]+iSeq+1);
// for (uint ii0=ind0+1; ii0<ii; ii0++) {//fill all the absent indices with this value
// SAi.writePacked(ii0,(indArray[2*iSeq]+iSeq+1) | mapGen.SAiMarkAbsentMaskC);
// };
// ++iSeq;
// ind0=ii;
// } else {
// iSeq=iSeq1;
// };
// } else
// {//index was present in the old genome
// while (iSeq<nInd && indArray[2*iSeq]+1<iSA2) {//for this index insert "smaller" junctions
// ++iSeq;
// };
//
// while (iSeq<nInd && indArray[2*iSeq]+1==iSA2) {//special case, the index falls right behind SAi
// if (funCalcSAi(seq1[0]+indArray[2*iSeq+1],iL) >= (int64) (ii-mapGen.genomeSAindexStart[iL]) ) {//this belongs to the next index
// break;
// };
// ++iSeq;
// };
//
// SAi.writePacked(ii,iSA1+iSeq);
//
// for (uint ii0=ind0+1; ii0<ii; ii0++) {//fill all the absent indices with this value
// SAi.writePacked(ii0,(iSA2+iSeq) | mapGen.SAiMarkAbsentMaskC);
// };
// ind0=ii;
// };
// };
//
// };
// // time ( &rawtime ); cout << timeMonthDayTime(rawtime) << "SAi first" <<endl;
//
// for (uint isj=0;isj<nInd;isj++) {
// int64 ind1=0;
// for (uint iL=0; iL < P.mapGen.gSAindexNbases; iL++) {
// uint g=(uint) seq1[0][indArray[2*isj+1]+iL];
// ind1 <<= 2;
// if (g>3) {//this iSA contains N, need to mark the previous
// for (uint iL1=iL; iL1 < P.mapGen.gSAindexNbases; iL1++) {
// ind1+=3;
// int64 ind2=mapGen.genomeSAindexStart[iL1]+ind1;
// for (; ind2>=0; ind2--) {//find previous index that is not absent
// if ( (SAi[ind2] & mapGen.SAiMarkAbsentMaskC)==0 ) {
// break;
// };
// };
// SAi.writePacked(ind2,SAi[ind2] | mapGen.SAiMarkNmaskC);
// ind1 <<= 2;
// };
// break;
// } else {
// ind1 += g;
// };
// };
// };
// time ( &rawtime );
// P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished SAi" <<endl;
//
// /* testing
// PackedArray SAio=SAi;
// SAio.allocateArray();
// ifstream oldSAiin("./DirTrue/SAindex");
// oldSAiin.read(SAio.charArray,8*(P.mapGen.gSAindexNbases+2));//skip first bytes
// oldSAiin.read(SAio.charArray,SAio.lengthByte);
// oldSAiin.close();
//
// for (uint iL=0; iL < P.mapGen.gSAindexNbases; iL++) {
// for (uint ii=mapGen.genomeSAindexStart[iL];ii<mapGen.genomeSAindexStart[iL+1]; ii++) {//scan through the longets index
// if ( SAio[ii]!=SAi[ii] ) {
// cout <<iL<<" "<<ii<<" "<<SAio[ii]<<" "<<SAi[ii]<<endl;
// };
// };
// };
// */
//change parameters, most parameters are already re-defined in sjdbPrepare.cpp
SA.defineBits(mapGen.GstrandBit+1,SA.length+nInd);//same as SA2
SA.pointArray(SA1.charArray);
mapGen.nSA=SA.length;
mapGen.nSAbyte=SA.lengthByte;
//generate SAi
genomeSAindex(G,SA,P,SAi,mapGen);
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " Finished SAi" <<endl;
// mapGen.sjGstart=mapGen.chrStart[mapGen.nChrReal];
// memcpy(G+mapGen.chrStart[mapGen.nChrReal],seq1[0], nseq1[0]);
return nInd;
};
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