Commit 2421a62d authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.6.0b+dfsg

parent e608df7f

CHANGES.md

+6 −0
Original line number Diff line number Diff line 
STAR 2.6.0b 2018/05/02

======================



* Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.5.0a.





STAR 2.6.0a 2018/04/23

======================

source/Parameters.cpp

+31 −4
Original line number Diff line number Diff line
@@ -889,6 +889,13 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters 
    };



    

     if (wasp.yes && outSAMtype.at(0)!="BAM") {

        ostringstream errOut;

        errOut <<"EXITING because of FATAL INPUT ERROR: --waspOutputMode requires output to BAM file\n";

        errOut <<"SOLUTION: re-run STAR with --waspOutputMode ... and --outSAMtype BAM ... \n";

        exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);

    };

    

    //outSAMattributes

    outSAMattrPresent.NH=false;//TODO re-write as class with constructor?

    outSAMattrPresent.HI=false;
@@ -1058,6 +1065,24 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters 
            exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);

    };

    

    if (pCh.multimapNmax>0 && (pCh.out.bam || pCh.out.samOld)) {       

            ostringstream errOut;

            errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions\n";

            errOut <<"SOLUTION: re-run with --chimOutType Junctions\n";

            exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);

    };

    

    if (peOverlap.NbasesMin > 0) {

        if (pCh.multimapNmax == 0 && (pCh.out.junctions || pCh.out.samOld)) {

                ostringstream errOut;

                errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax 0 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType WithinBAM\n";

                errOut <<"SOLUTION: re-run with --chimOutType WithinBAM\n";

                exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);

        };

    };

        

    

    

    if (pCh.out.bam && !outSAMattrPresent.NM) {

       outSAMattrOrder.push_back(ATTR_NM);

       inOut->logMain << "WARNING --chimOutType=WithinBAM, therefore STAR will output NM attribute" <<endl;
@@ -1217,8 +1242,8 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters 


        if (pGe.gLoad!="NoSharedMemory") {

            ostringstream errOut;

            errOut << "EXITING because of fatal PARAMETERS error: 2-pass method is not compatible with pGe.gLoad<<"<<pGe.gLoad<<"\n";

            errOut << "SOLUTION: re-run STAR with --genomeLoad NoSharedMemory ; this is the only compatible option at the moment.s\n";

            errOut << "EXITING because of fatal PARAMETERS error: 2-pass method is not compatible with --genomeLoad "<<pGe.gLoad<<"\n";

            errOut << "SOLUTION: re-run STAR with --genomeLoad NoSharedMemory ; this is the only option compatible with --twopassMode Basic .\n";

            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);

        };

        twoPass.yes=true;
@@ -1359,6 +1384,8 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters 
    //peOverlap

    if (peOverlap.NbasesMin>0) {

        peOverlap.yes=true;

    } else {

        peOverlap.yes=false;

    };

    

    ////////////////////////////////////////////////

source/ReadAlign_chimericDetectionOldOutput.cpp

+32 −28
Original line number Diff line number Diff line
@@ -78,7 +78,7 @@ void ReadAlign::chimericDetectionOldOutput() { 


            };



            bamN+=alignBAM(trChim[itr], 1, 0, mapGen.chrStart[trChim[itr].Chr],  mateChr, mateStart-mapGen.chrStart[mateChr], mateStrand, \

            bamN+=alignBAM(trChim[itr], 1, 0, mapGen.chrStart[trChim[itr].Chr],  mateChr, mateStart-mapGen.chrStart[(mateChr<mapGen.nChrReal ? mateChr : 0)], mateStrand, \

                            alignType, NULL, P.outSAMattrOrder, outBAMoneAlign+bamN, outBAMoneAlignNbytes+bamN);

            bamBytesTotal+=outBAMoneAlignNbytes[0]+outBAMoneAlignNbytes[1];//outBAMoneAlignNbytes[1] = 0 if SE is recorded

        };
@@ -110,7 +110,7 @@ void ReadAlign::chimericDetectionOldOutput() { 
        };

    };





    if (P.pCh.out.samOld) {

        for (uint iTr=0;iTr<chimN;iTr++) 

        {//write all chimeric pieces to Chimeric.out.sam/junction

            if (P.readNmates==2) {//PE: need mate info
@@ -134,6 +134,9 @@ void ReadAlign::chimericDetectionOldOutput() { 
                outputTranscriptSAM(trChim[iTr], chimN, iTr, -1, -1, -1, -1, NULL, &chunkOutChimSAM);

            };

        };

    };

    

    if (P.pCh.out.junctions) {

        //junction + SAMp

        *chunkOutChimJunction << mapGen.chrName[trChim[0].Chr] <<"\t"<< chimJ0 - mapGen.chrStart[trChim[0].Chr]+1 <<"\t"<< (trChim[0].Str==0 ? "+":"-") \

                <<"\t"<< mapGen.chrName[trChim[1].Chr] <<"\t"<< chimJ1 - mapGen.chrStart[trChim[1].Chr]+1 <<"\t"<< (trChim[1].Str==0 ? "+":"-") \
@@ -143,6 +146,7 @@ void ReadAlign::chimericDetectionOldOutput() { 
        if (P.outSAMattrPresent.RG)

            *chunkOutChimJunction <<"\t"<< P.outSAMattrRG.at(readFilesIndex);

        *chunkOutChimJunction <<"\n"; //<<"\t"<< trChim[0].exons[0][EX_iFrag]+1 --- no need for that, since trChim[0] is always on the first mate

    };

    

    return;

};
 
 No newline at end of file

source/ReadAlign_peOverlapMergeMap.cpp

+17 −12
Original line number Diff line number Diff line
@@ -3,9 +3,9 @@ 


void ReadAlign::peOverlapMergeMap() {

    

    peOv.yes=false;



    if (!P.peOverlap.yes || P.readNmates!=2 ) {//no peOverlap

        peOv.yes=false;

        return;

    };
@@ -18,10 +18,9 @@ void ReadAlign::peOverlapMergeMap() { 
    peMergeRA->peMergeMates();

    peOv=peMergeRA->peOv;





    

    if (peOv.nOv==0) {//check if mates can be merged, if not - return

        //cout <<"\n-1\n";

        peOv.yes=false;

        return;

    };
@@ -74,6 +73,8 @@ void ReadAlign::peOverlapMergeMap() { 
    

    if (peScore<=trBest->maxScore || chimRecord) {

        peOv.yes=true;

    } else {

        peOv.yes=false;

    };

    

    return;
@@ -202,12 +203,13 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig 


            exons[nExons][EX_iFrag]=(imate==0 ? t.Str : 1-t.Str);

            exons[nExons][EX_sjA]=t.exons[iex][EX_sjA];

            canonSJ[nExons]=t.canonSJ[iex];

            sjAnnot[nExons]=t.sjAnnot[iex];

            sjStr[nExons]=t.sjStr[iex];

            shiftSJ[nExons][0]=t.shiftSJ[iex][0];

            shiftSJ[nExons][1]=t.shiftSJ[iex][1];



            if (nExons>0 && iex>0) {

                canonSJ[nExons-1]=t.canonSJ[iex-1];

                sjAnnot[nExons-1]=t.sjAnnot[iex-1];

                sjStr[nExons-1]=t.sjStr[iex-1];

                shiftSJ[nExons-1][0]=t.shiftSJ[iex-1][0];

                shiftSJ[nExons-1][1]=t.shiftSJ[iex-1][1];

            };

            //record these exons for mate2

            if (t.exons[iex][EX_R]>=mSta[imate]) {//exon left is inside the mate

                exons[nExons][EX_G]=t.exons[iex][EX_G];
@@ -227,9 +229,12 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig 
            ++nExons;

        };

        canonSJ[nExons-1]=-3; //marks "junction" between mates

        sjAnnot[nExons-1]=0;

        sjStr[nExons-1]=0;

        shiftSJ[nExons-1][0]=0;

        shiftSJ[nExons-1][1]=0;

    }; 

    

    

    //copy scalar variables

    for (uint ii=0;ii<3;ii++) {

        intronMotifs[ii]=t.intronMotifs[ii];

source/VERSION

+1 −1
Original line number Diff line number Diff line 
#define STAR_VERSION "STAR_2.6.0a"
 
#define STAR_VERSION "STAR_2.6.0b"