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#include "genomeSAindex.h"
#include "TimeFunctions.h"
#include "SuffixArrayFuns.h"
#include "ErrorWarning.h"
void genomeSAindex(char * G, PackedArray & SA, Parameters & P, PackedArray & SAi, Genome &mapGen)
{
mapGen.genomeSAindexStart = new uint [mapGen.pGe.gSAindexNbases+1];
mapGen.genomeSAindexStart[0]=0;
for (uint ii=1;ii<=mapGen.pGe.gSAindexNbases;ii++) {//L-mer indices starts
mapGen.genomeSAindexStart[ii] = mapGen.genomeSAindexStart[ii-1] + ( 1LLU<<(2*ii) );
};
mapGen.nSAi = mapGen.genomeSAindexStart[mapGen.pGe.gSAindexNbases];
/* testing
// uint* SAi1=new uint[mapGen.nSAi];
PackedArray SAio;
SAio.defineBits(mapGen.GstrandBit+3,mapGen.nSAi);
SAio.allocateArray();
ifstream oldSAiin("./DirTrue/SAindex");
oldSAiin.read(SAio.charArray,8*(mapGen.pGe.gSAindexNbases+2));//skip first bytes
oldSAiin.read(SAio.charArray,SAio.lengthByte);
oldSAiin.close();
*/
mapGen.SAiMarkNbit=mapGen.GstrandBit+1;
mapGen.SAiMarkAbsentBit=mapGen.GstrandBit+2;
mapGen.SAiMarkNmaskC=1LLU << mapGen.SAiMarkNbit;
mapGen.SAiMarkNmask=~mapGen.SAiMarkNmaskC;
mapGen.SAiMarkAbsentMaskC=1LLU << mapGen.SAiMarkAbsentBit;
mapGen.SAiMarkAbsentMask=~mapGen.SAiMarkAbsentMaskC;
SAi.defineBits(mapGen.GstrandBit+3,mapGen.nSAi);
SAi.allocateArray();
time_t rawTime;
time(&rawTime);
P.inOut->logMain << timeMonthDayTime(rawTime) <<" ... generating Suffix Array index\n" <<flush;
*P.inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... generating Suffix Array index\n" <<flush;
/*testing
PackedArray SA1=SA;
uint* ind0=new uint[mapGen.pGe.gSAindexNbases];
for (uint ii=0; ii<mapGen.pGe.gSAindexNbases; ii++) {
ind0[ii]=-1;//this is needed in case "AAA...AAA",i.e. indPref=0 is not present in the genome for some lengths
};
uint* SAi1=new uint[mapGen.nSAi];
for (uint isa=0; isa<mapGen.nSA; isa++) {//for all suffixes
if (isa%100000000==0) P.inOut->logMain << isa*100/mapGen.nSA << "% " << flush;
uint SAstr=SA1[isa];
bool dirG = (SAstr>>mapGen.GstrandBit) == 0; //forward or reverse strand of the genome
SAstr &= mapGen.GstrandMask;
if (!dirG) SAstr=mapGen.nGenome-1-SAstr;
uint indPref=0;
for (uint iL=0; iL < mapGen.pGe.gSAindexNbases; iL++) {//calculate index
indPref <<= 2;
uint g1= (uint) G[dirG ? SAstr+iL : SAstr-iL]; //reverese if (-) strand
if (g1>3) {//if N, this suffix does not belong in SAi
for (uint iL1=iL; iL1 < mapGen.pGe.gSAindexNbases; iL1++) {
SAi1[mapGen.genomeSAindexStart[iL1]+ind0[iL1]] |= mapGen.SAiMarkNmaskC;
};
break;
};
if (!dirG) g1=3-g1; //complement if (-) strand
indPref += (uint) g1;
if ( indPref > ind0[iL] || isa==0 ) {//new && good index, record it
SAi1[mapGen.genomeSAindexStart[iL]+indPref]=isa;
for (uint ii=ind0[iL]+1; ii<indPref; ii++) {//index is not present, record to the last present suffix
SAi1[mapGen.genomeSAindexStart[iL]+ii] = isa | mapGen.SAiMarkAbsentMaskC;
};
ind0[iL]=indPref;
} else if ( indPref < ind0[iL] ) {
ostringstream errOut;
errOut << "BUG: next index is smaller than previous, EXITING\n" <<flush;
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
};
};//for (uint isa=0; isa<mapGen.nSA; isa++)
*/
genomeSAindexChunk(G, SA, P, SAi, 0, SA.length-1, mapGen);
time(&rawTime);
P.inOut->logMain << timeMonthDayTime(rawTime) <<" ... completed Suffix Array index\n" <<flush;
*P.inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... completed Suffix Array index\n" <<flush;
// for (uint ii=1;ii<=mapGen.pGe.gSAindexNbases-1;ii++) {//L-mer indices starts
// cout <<ii<<endl;
// for (uint jj=mapGen.genomeSAindexStart[ii-1]; jj<mapGen.genomeSAindexStart[ii]; jj++)
// {
// if (SAi[jj]!=SAio[jj])
// {
// cout <<ii <<" "<< jj<<" "<<jj-mapGen.genomeSAindexStart[ii-1]<<" "<<SAi[jj]<<" "<<SAio[jj]<<" "<<endl;
// sleep(100);
// };
// };
// };
};
void genomeSAindexChunk(char * G, PackedArray & SA, Parameters & P, PackedArray & SAi, uint iSA1, uint iSA2, Genome &mapGen)
{
uint* ind0=new uint[mapGen.pGe.gSAindexNbases];
for (uint ii=0; ii<mapGen.pGe.gSAindexNbases; ii++) {
ind0[ii]=-1;//this is needed in case "AAA...AAA",i.e. indPref=0 is not present in the genome for some lengths
};
PackedArray SAi1;
SAi1=SAi;
SAi1.allocateArray();
uint isaStep=mapGen.nSA/(1llu<<(2*mapGen.pGe.gSAindexNbases))+1;
// isaStep=8;
uint isa=iSA1;
int iL4;
uint indFull=funCalcSAiFromSA(G,SA,mapGen,isa,mapGen.pGe.gSAindexNbases,iL4);
while (isa<=iSA2) {//for all suffixes
for (uint iL=0; iL < mapGen.pGe.gSAindexNbases; iL++) {//calculate index
uint indPref = indFull >> (2*(mapGen.pGe.gSAindexNbases-1-iL));
if ( (int)iL==iL4 ) {//this suffix contains N and does not belong in SAi
for (uint iL1=iL; iL1 < mapGen.pGe.gSAindexNbases; iL1++) {
SAi.writePacked(mapGen.genomeSAindexStart[iL1]+ind0[iL1],SAi[mapGen.genomeSAindexStart[iL1]+ind0[iL1]] | mapGen.SAiMarkNmaskC);
};
break;//break the iL cycle
};
if ( indPref > ind0[iL] || isa==0 ) {//new && good index, record it
SAi.writePacked(mapGen.genomeSAindexStart[iL]+indPref, isa);
for (uint ii=ind0[iL]+1; ii<indPref; ii++) {//index is not present, record to the last present suffix
SAi.writePacked(mapGen.genomeSAindexStart[iL]+ii, isa | mapGen.SAiMarkAbsentMaskC);
};
ind0[iL]=indPref;
} else if ( indPref < ind0[iL] ) {
ostringstream errOut;
errOut << "BUG: next index is smaller than previous, EXITING\n" <<flush;
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
};
//find next index not equal to the current one
funSAiFindNextIndex(G, SA, isaStep, isa, indFull, iL4, mapGen);//indFull and iL4 have been already defined at the previous step
};//isa cycle
for (uint iL=0; iL < mapGen.pGe.gSAindexNbases; iL++) {//fill up unfilled indexes
for (uint ii=mapGen.genomeSAindexStart[iL]+ind0[iL]+1; ii<mapGen.genomeSAindexStart[iL+1]; ii++) {
SAi.writePacked(ii, mapGen.nSA | mapGen.SAiMarkAbsentMaskC);
};
};
delete [] ind0;
};
void funSAiFindNextIndex(char * G, PackedArray & SA, uint isaStep, uint & isa, uint & indFull, int & iL4, Genome &mapGen)
{
uint indFullPrev=indFull;
int iL4prev=iL4;
isa+=isaStep;
while (isa<mapGen.nSA && (indFull=funCalcSAiFromSA(G,SA,mapGen,isa,mapGen.pGe.gSAindexNbases,iL4))==indFullPrev && iL4==iL4prev)
{//make large step in isa while the indFull/iL4 are still the same
isa+=isaStep;
};
if (isa>=mapGen.nSA)
{//reached the end of the SA
indFull=funCalcSAiFromSA(G,SA,mapGen,mapGen.nSA-1,mapGen.pGe.gSAindexNbases,iL4);
if (indFull==indFullPrev && iL4==iL4prev)
{
isa=mapGen.nSA;//no more indices, the last one is equal to the previous
return;
};
};
{//binary search
uint i1=isa-isaStep;
uint i2=min(isa,mapGen.nSA-1);
while (i1+1<i2)
{
isa=i1/2 + i2/2 + (i1%2 + i2%2)/2;
if ((indFull=funCalcSAiFromSA(G,SA,mapGen,isa,mapGen.pGe.gSAindexNbases,iL4))==indFullPrev && iL4==iL4prev)
{
i1=isa;
} else
{
i2=isa;
};
};
if (isa==i1)
{
isa=i2;
indFull=funCalcSAiFromSA(G,SA,mapGen,isa,mapGen.pGe.gSAindexNbases,iL4);
};
};
};
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