CHANGES.md

+STAR 2.6.1a 2018/08/14
+======================
+
+* Process substitution can now be used with zipped VCF files, e.g. --varVCFfile <(zcat vcf.gz)
+* Implemented fatal error exception if no SNPs are found in VCF files.
+* Implemented --chimOutJunctionFormat 1 option to output some metadata (command lines and basic mapping statistics) at the end of Chimeric.out.junction file.
+* The default value of --peOverlapMMp is reduced to 0.01 for less aggressive mate merging.
+* Fixed the problem with control characters (ASCII<32) in genome and input read sequences. They used to be converted to N, now they are removed.
+* Fixed a bug that caused serious problems with --sjdbInsertSave All option.
+* Fixed a bug in merging mates (--peOverlap*) algorithm that was causing rare seg-faults.
+* Fixed the GtstrandBit problem.
+* Fixed a bug with multiple RG lines when inputting reads in SAM format.
+* Fixed a bug causing seg-faults with shared memory and --outStd options.
+* Fixed a bug with --outTmpDir and fifo files.
+
 STAR 2.6.0c 2018/05/10
 ======================
 

README.md

@@ -41,6 +41,7 @@ cd STAR-2.6.0a
 
 # Alternatively, get STAR source using git
 git clone https://github.com/alexdobin/STAR.git
+```
 
 Compile under Linux
 -------------------

debian/changelog

+rna-star (2.6.1a+dfsg-1) unstable; urgency=medium
+
+  * New upstream release.
+  * Fix spelling via patches.
+
+ -- Sascha Steinbiss <satta@debian.org>  Sat, 18 Aug 2018 16:14:17 +0200
+
 rna-star (2.6.0c+dfsg-1) unstable; urgency=medium
 
   * New upstream release.

debian/patches/series

 donotuse_own_htslib.patch
 mips_shm_noreserve.patch
 reproducible.patch
+spelling.patch

debian/patches/spelling.patch

+Description: fix spelling
+Author: Sascha Steinbiss <satta@debian.org>
+Forwarded: https://github.com/alexdobin/STAR/pull/475
+--- a/extras/doc-latex/parametersDefault.tex
++++ b/extras/doc-latex/parametersDefault.tex
+@@ -715,7 +715,7 @@
+   \optLine{int{\textgreater}=0: the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax {\textgreater} 1} 
+ \optName{chimNonchimScoreDropMin}
+   \optValue{20}
+-  \optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read lenght has to be smaller than this value} 
++  \optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be smaller than this value} 
+ \optName{chimOutJunctionFormat}
+   \optValue{0}
+   \optLine{int: formatting type for the Chimeric.out.junction file} 
+--- a/source/Genome.cpp
++++ b/source/Genome.cpp
+@@ -547,7 +547,7 @@
+         P.winBinNbits = (uint) floor( log2( max( max(4LLU,P.alignIntronMax), (P.alignMatesGapMax==0 ? 1000LLU : P.alignMatesGapMax) ) /4 ) + 0.5);
+         P.winBinNbits = max( P.winBinNbits, (uint) floor(log2(nGenome/40000+1)+0.5) ); 
+         //ISSUE - to be fixed in STAR3: if alignIntronMax>0 but alignMatesGapMax==0, winBinNbits will be defined by alignIntronMax
+-        P.inOut->logMain << "To accomodate alignIntronMax="<<P.alignIntronMax<<" redefined winBinNbits="<< P.winBinNbits <<endl;
++        P.inOut->logMain << "To accommodate alignIntronMax="<<P.alignIntronMax<<" redefined winBinNbits="<< P.winBinNbits <<endl;
+ 
+     };
+ 
+--- a/source/ReadAlign_stitchWindowSeeds.cpp
++++ b/source/ReadAlign_stitchWindowSeeds.cpp
+@@ -255,7 +255,7 @@
+ //         };
+ 
+ 
+-        //check exons lenghts including repeats, do not report a transcript with short exons
++        //check exons lengths including repeats, do not report a transcript with short exons
+ //        for (uint isj=0;isj<trA.nExons-1;isj++) {//check exons for min length, if they precede a junction
+ //            if ( trA.canonSJ[isj]>=0 &&
+ //               ( trA.exons[isj][EX_L] < P.alignSJoverhangMin + trA.shiftSJ[isj][0]
+--- a/source/parametersDefault
++++ b/source/parametersDefault
+@@ -619,7 +619,7 @@
+     int>=0: the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax > 1
+ 
+ chimNonchimScoreDropMin         20
+-    int>=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read lenght has to be smaller than this value
++    int>=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be smaller than this value
+ 
+ chimOutJunctionFormat           0
+     int: formatting type for the Chimeric.out.junction file
+--- a/source/stitchWindowAligns.cpp
++++ b/source/stitchWindowAligns.cpp
+@@ -93,7 +93,7 @@
+         };
+         trA.gLength = tG2+1-trA.gStart;
+ 
+-        //check exons lenghts including repeats, do not report a transcript with short exons
++        //check exons lengths including repeats, do not report a transcript with short exons
+         for (uint isj=0;isj<trA.nExons-1;isj++) {//check exons for min length, if they are not annotated and precede a junction
+             if ( trA.canonSJ[isj]>=0 ) {//junction
+                 if (trA.sjAnnot[isj]==1) {//sjdb

extras/doc-latex/STARmanual.tex

@@ -34,7 +34,7 @@
 
 \newcommand{\sechyperref}[1]{\hyperref[#1]{Section \ref{#1}. \nameref{#1}}}
 
-\title{STAR manual 2.6.0a}
+\title{STAR manual 2.6.1a}
 \author{Alexander Dobin\\
 dobin@cshl.edu}
 \maketitle
@@ -273,7 +273,7 @@ The SAM attributes can be specified by the user using \opt{outSAMattributes} \op
 \item[]
 \optv{NH HI NM MD} have standard meaning as defined in the SAM format specifications.
 \item[]
-\optv{AS} id the local alignment score (paired for paired-edn reads). 
+\optv{AS} id the local alignment score (paired for paired-end reads). 
 \item[]
 \optv{nM} is the number of mismatches per (paired) alignment, not to be confused with \optv{NM}, which is the number of mismatches in each mate.
 \item[]
@@ -335,11 +335,11 @@ STAR-Fusion is a software package for detecting fusion transcript from STAR chim
 Chimeric alignments can be included together with normal alignments in the main (sorted or unsorted) BAM file(s) using \opt{chimOutType} \optv{WithinBAM}. In these files, formatting of chimeric alignments follows the latest SAM/BAM specifications.
    
 \subsection{Chimeric alignments in \ofilen{Chimeric.out.sam} .}
-When chimeric detection is switched on, STAR will output normal alignments into \ofilen{Aligned.*.sam/bam}, and will output chimeric alignments into a separate file \ofilen{Chimeric.out.sam}. 
+With \opt{chimOutType} \optv{SeparateSAMold} STAR will output normal alignments into \ofilen{Aligned.*.sam/bam}, and will output chimeric alignments into a separate file \ofilen{Chimeric.out.sam}. Note that this option will be deprecated in the future, and the \opt{chimOutType} \optv{WithinBAM} is strongly recommended.
 Some reads may be output to both normal SAM/BAM files, and \ofilen{Chimeric.out.sam} for the following reason. STAR will output a non-chimeric alignment into \ofilen{Aligned.out.sam} with soft-clipping a portion of the read. If this portion is long enough, and it maps well and uniquely  somewhere else in the genome, there will also be a chimeric alignment output into \ofilen{Chimeric.out.sam}. For instance, if you have a paired-end read where the second mate can be split chimerically into 70 and 30 bases. The 100b of the first mate + 70b of the 2nd mate map non-chimerically,and the mapping length/score are big enough, so they will be output into \ofilen{Aligned.out.sam} file. At the same time, the chimeric segments 100-mate1 + 70-mate2 and 30-mate2 will be output into \ofilen{Chimeric.out.sam}.
 
 \subsection{Chimeric alignments in \ofilen{Chimeric.out.junction}}
-In addition to \ofilen{Chimeric.out.sam}, STAR will generate \ofilen{Chimeric.out.junction} file which maybe more convenient for downstream analysis.
+By default, or with \opt{chimOutType} \optv{Junctions}, STAR will generate \ofilen{Chimeric.out.junction} file which maybe more convenient for downstream analysis.
 The format of this file is as follows. Every line contains one chimerically aligned read, e.g.:
 \begin{verbatim}
 chr22   23632601        +       chr9    133729450       +       1       0       0      

extras/doc-latex/parametersDefault.tex

@@ -637,7 +637,7 @@
   \optValue{0}
   \optLine{int{\textgreater}=0:             minimum number of overlap bases to trigger mates merging and realignment} 
 \optName{peOverlapMMp}
-  \optValue{0.1}
+  \optValue{0.01}
   \optLine{real, {\textgreater}=0 {\&} {\textless}1:     maximum proportion of mismatched bases in the overlap area} 
 \end{optTable}
 \optSection{Windows, Anchors, Binning}\label{Windows,_Anchors,_Binning}
@@ -716,6 +716,13 @@
 \optName{chimNonchimScoreDropMin}
   \optValue{20}
   \optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read lenght has to be smaller than this value} 
+\optName{chimOutJunctionFormat}
+  \optValue{0}
+  \optLine{int: formatting type for the Chimeric.out.junction file} 
+\begin{optOptTable}
+  \optOpt{0}   \optOptLine{no comment lines/headers}
+  \optOpt{1}   \optOptLine{comment lines at the end of the file: command line and Nreads: total, unique, multi}
+\end{optOptTable}
 \end{optTable}
 \optSection{Quantification of Annotations}\label{Quantification_of_Annotations}
 \begin{optTable}

extras/scripts/filterCirc.awk

@@ -20,7 +20,7 @@ if ( $7>=0 && $1==$4 && $3==$6 && (($3=="-" && $5>$2 && $5-$2<1000000) || ($3=="
 	#print $11,$11+cigarGenomicDist($12),$13,$13+cigarGenomicDist($14);
         if ( ($3=="+" && $11+endTol>$5 && $13+cigarGenomicDist($14)-endTol<=$2) \
           || ($3=="-" && $13+endTol>$2 && $11+cigarGenomicDist($12)-endTol<=$5) ) {  
-               print $1,($3=="+"?$5:$2),($3=="+"?$2:$5),($3=="+"?"-":"+"),($7==0?0:3-$7),$8,$9;
+               print $1,($3=="+"?$5:$2),($3=="+"?$2:$5),($3=="+"?"-":"+"),($7==0?0:3-$7),$8,$9,(NF>=15 ? $NF:1);
 	};
 };
 };

extras/scripts/mergeGeneCounts.awk

+#
+# merges ReadsPerGene.out.tab files from multiple runs into one table
+# usage:
+# awk -f mergeGeneCounts.awk -v Col=2 /path/to/1st/ReadsPerGene.out.tab /path/to/2nd/ReadsPerGene.out.tab ...
+# e.g.
+# awk -f mergeGeneCounts.awk -v Col=2 */ReadsPerGene.out.tab
+#
+# -v Col=<column to add to the table>: depends on the standedness of the table
+# advanced parameters
+# -v Skip=<number of lines to skip>
+# -v Name=<common file name substring to remove from column names>
+
+
+
+
+BEGIN {
+    FS="\t";
+
+    if (Name=="") Name="/ReadsPerGene.out.tab";
+    if (Skip=="") Skip=0;
+    if (Col=="") {
+        print "Specify the column with -v Col=..." > /dev/err;
+        exit;
+    };
+
+    for (jj=1;jj<=ARGC;jj++)
+    {# print header line with file names
+        a=ARGV[jj]; 
+        gsub(Name,"",a);
+        printf ";" a
+    }; 
+    printf "\n";
+} 
+{
+    if (ARGIND==1) {
+        L[FNR]=$1; # record gene names (1st column)
+    } else {
+        if ($1!=L[FNR]) {
+            print "File #" ARGIND ": " FILENAME " is not sorted properly, sort all files by the first column" >/dev/err;
+        };
+    };
+
+    V[FNR,ARGIND]=$2
+} 
+END {
+    for (ii=1;ii<=length(L);ii++) 
+    {
+        printf "%s",L[ii];
+        if (V[ii,1]!="") 
+            for (jj=1;jj<=ARGC;jj++) 
+                printf ";" V[ii,jj]; 
+        printf "\n"
+     } 
+}

extras/scripts/sjFromSAMcollapseUandM.awk

@@ -21,7 +21,7 @@ if (substr($1,1,1)!="@") {
         } else if (C[k+1]=="N") {
            sj1=$3 "\t" g "\t" g+L[k]-1;
            readSJs[sj1]++;
-           if (readSJs[sj1]==1) {#only count this junction if it has nto been counted for the same read
+           if (readSJs[sj1]==1) {#only count this junction if it has not been counted for the same read
                SJ[sj1]=1;
                if ($5>=mapqU) {
                    SJu[sj1]++;

extras/scripts/sjFromSAMcollapseUandM_inclOverlaps.awk

@@ -22,7 +22,7 @@ if (substr($1,1,1)!="@") {
            sj1=$3 "\t" g "\t" g+L[k]-1;
            readSJs[sj1]++;
 
-           if (readSJs[sj1]==1) {#only count this junction if it has nto been counted for the same read
+           if (readSJs[sj1]==1) {#only count this junction if it has not been counted for the same read
                SJ[sj1]=1;
                if ($5>=mapqU) {
                    SJu[sj1]++;

source/BAMbinSortByCoordinate.cpp

@@ -49,6 +49,13 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st
 
     BGZF *bgzfBin;
     bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P.outBAMcompression)).c_str());
+    if (bgzfBin==NULL) {
+        ostringstream errOut;
+        errOut <<"EXITING because of fatal ERROR: could not open temporary bam file: " << dirBAMsort+"/b"+to_string((uint) iBin) << "\n";
+        errOut <<"SOLUTION: check that the disk is not full, increase the max number of open files with Linux command ulimit -n before running STAR";
+        exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
+    };
+    
     outBAMwriteHeader(bgzfBin,P.samHeaderSortedCoord,mapGen.chrNameAll,mapGen.chrLengthAll);
     //send ordered aligns to bgzf one-by-one
     for (uint ia=0;ia<binN;ia++) {

source/BAMbinSortUnmapped.cpp

@@ -6,6 +6,13 @@ void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, Parameter
 
     BGZF *bgzfBin;
     bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P.outBAMcompression)).c_str());
+    if (bgzfBin==NULL) {
+        ostringstream errOut;
+        errOut <<"EXITING because of fatal ERROR: could not open temporary bam file: " << dirBAMsort+"/b"+to_string((uint) iBin) << "\n";
+        errOut <<"SOLUTION: check that the disk is not full, increase the max number of open files with Linux command ulimit -n before running STAR";
+        exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
+    };
+        
     outBAMwriteHeader(bgzfBin,P.samHeaderSortedCoord,mapGen.chrNameAll,mapGen.chrLengthAll);
 
 

source/Genome.cpp

@@ -32,12 +32,12 @@ Genome::Genome (Parameters &Pin ): pGe(Pin.pGe), P(Pin), shmStart(NULL), sharedM
     sjdbLength = pGe.sjdbOverhang==0 ? 0 : pGe.sjdbOverhang*2+1;   
 };
 
-Genome::~Genome()
-{
-    if (sharedMemory != NULL)
-        delete sharedMemory;
-    sharedMemory = NULL;
-}
+// Genome::~Genome()
+// {
+//     if (sharedMemory != NULL)
+//         delete sharedMemory;
+//     sharedMemory = NULL;
+// }
 
 void Genome::freeMemory(){//free big chunks of memory used by genome and suffix array
 

source/Genome.h

@@ -45,8 +45,10 @@ class Genome {
         uint genomeInsertL; //total length of the sequence to be inserted on the fly
         uint genomeInsertChrIndFirst; //index of the first inserted chromosome
 
+        SharedMemory * sharedMemory;
+        
         Genome (Parameters &Pin );
-        ~Genome();
+        //~Genome();
 
         void freeMemory();
         void genomeLoad();
@@ -62,7 +64,6 @@ class Genome {
         key_t shmKey;
         char *shmStart;
         char *G1; //pointer -200 of G        
-        SharedMemory * sharedMemory;
         uint OpenStream(string name, ifstream & stream, uint size);
         void HandleSharedMemoryException(const SharedMemoryException & exc, uint64 shmSize);
 

source/Genome_genomeGenerate.cpp

@@ -238,8 +238,10 @@ void Genome::genomeGenerate() {
         };
     };
 
-    GstrandBit = (uint) floor(log(N+P.limitSjdbInsertNsj*sjdbLength)/log(2))+1;
+    GstrandBit = (char) (uint) floor(log(N+P.limitSjdbInsertNsj*sjdbLength)/log(2))+1;
     if (GstrandBit<32) GstrandBit=32; //TODO: use simple access function for SA
+    P.inOut->logMain <<"Estimated genome size="<<N+P.limitSjdbInsertNsj*sjdbLength<<"   "<<N<<"   "<<P.limitSjdbInsertNsj*sjdbLength<<"\n";
+    P.inOut->logMain << "GstrandBit=" << int(GstrandBit) <<"\n";
 
     GstrandMask = ~(1LLU<<GstrandBit);
     SA.defineBits(GstrandBit+1,nSA);
@@ -445,9 +447,6 @@ void Genome::genomeGenerate() {
 
         sjdbInsertJunctions(P, *this, mainGenome1, sjdbLoci);
 
-        //write an extra 0 at the end of the array, filling the last bytes that otherwise are not accessible, but will be written to disk
-        //this is - to avoid valgrind complaints. Note that SApass1 is allocated with plenty of space to spare.
-        SA.writePacked(nSA,0);
     };
 
     pGe.gFileSizes.clear();

source/InOutStreams.cpp

@@ -23,12 +23,13 @@ InOutStreams::~InOutStreams() {
     logFinal.flush();
     outLocalChains.flush();
 
-    logStdOutFile.close();
+    //logStdOutFile.close(); //do not want to close these log files, as some destructors (e.g. ~SharedMemory) might still write there
+    //logMain.close();
+    
     outSAMfile.close();
     outChimSAM.close();
     outChimJunction.close();
     logProgress.close();
-    logMain.close();
     logFinal.close();
     outLocalChains.close();
 

source/Parameters.cpp

@@ -217,6 +217,7 @@ Parameters::Parameters() {//initalize parameters info
     parArray.push_back(new ParameterInfoScalar <uint>       (-1, -1, "chimMultimapNmax", &pCh.multimapNmax));
     parArray.push_back(new ParameterInfoScalar <uint>       (-1, -1, "chimMultimapScoreRange", &pCh.multimapScoreRange));
     parArray.push_back(new ParameterInfoScalar <uint>       (-1, -1, "chimNonchimScoreDropMin", &pCh.nonchimScoreDropMin));
+    parArray.push_back(new ParameterInfoVector <int>        (-1, -1, "chimOutJunctionFormat", &pCh.outJunctionFormat));
 
     //sjdb
     parArray.push_back(new ParameterInfoVector <string> (-1, -1, "sjdbFileChrStartEnd", &pGe.sjdbFileChrStartEnd));
@@ -453,7 +454,7 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
         outFileTmp=outFileNamePrefix +"_STARtmp/";
         sysRemoveDir (outFileTmp);
     } else {
-        outFileTmp=outTmpDir;
+        outFileTmp=outTmpDir + "/";
     };
 
     if (mkdir (outFileTmp.c_str(),runDirPerm)!=0) {
@@ -777,6 +778,60 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
         };
     };
 
+    //two-pass
+    if (parArray.at(twoPass.pass1readsN_par)->inputLevel>0  && twoPass.mode=="None")
+    {
+        ostringstream errOut;
+        errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN is defined, but --twoPassMode is not defined\n";
+        errOut << "SOLUTION: to activate the 2-pass mode, use --twopassMode Basic";
+        exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+    };
+
+    twoPass.yes=false;
+    twoPass.pass2=false;
+    if (twoPass.mode!="None") {//2-pass parameters
+        if (runMode!="alignReads")
+        {
+            ostringstream errOut;
+            errOut << "EXITING because of fatal PARAMETERS error: 2-pass mapping option  can only be used with --runMode alignReads\n";
+            errOut << "SOLUTION: remove --twopassMode option";
+            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+        };
+
+        if (twoPass.mode!="Basic")
+        {
+            ostringstream errOut;
+            errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --twopassMode="<<twoPass.mode<<"\n";
+            errOut << "SOLUTION: for the 2-pass mode, use allowed values --twopassMode: Basic";
+            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+        };
+
+        if (twoPass.pass1readsN==0)
+        {
+            ostringstream errOut;
+            errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN = 0 in the 2-pass mode\n";
+            errOut << "SOLUTION: for the 2-pass mode, specify --twopass1readsN > 0. Use a very large number or -1 to map all reads in the 1st pass.\n";
+            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+        };
+
+        if (pGe.gLoad!="NoSharedMemory") {
+            ostringstream errOut;
+            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;
+        twoPass.dir=outFileNamePrefix+"_STARpass1/";
+        sysRemoveDir (twoPass.dir);
+        if (mkdir (twoPass.dir.c_str(),runDirPerm)!=0) {
+            ostringstream errOut;
+            errOut <<"EXITING because of fatal ERROR: could not make pass1 directory: "<< twoPass.dir<<"\n";
+            errOut <<"SOLUTION: please check the path and writing permissions \n";
+            exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+        };
+    };   
+    
+    // openReadFiles depends on twoPass for reading SAM header
     if (runMode=="alignReads" && pGe.gLoad!="Remove" && pGe.gLoad!="LoadAndExit") {//open reads files to check if they are present
         openReadsFiles();
 
@@ -924,7 +979,7 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
     vector<string> vAttr1;
     if (outSAMattributes.at(0)=="None") {
     } else if (outSAMattributes.at(0)=="All"){
-        vAttr1={"NH","HI","AS","nM","NM","MD","jM","jI","rB","MC","ch"};
+        vAttr1={"NH","HI","AS","nM","NM","MD","jM","jI","MC","ch"};
     } else if (outSAMattributes.at(0)=="Standard"){
         vAttr1={"NH","HI","AS","nM"};
     } else {
@@ -1203,61 +1258,6 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
         };
     };
 
-
-    //two-pass
-    if (parArray.at(twoPass.pass1readsN_par)->inputLevel>0  && twoPass.mode=="None")
-    {
-        ostringstream errOut;
-        errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN is defined, but --twoPassMode is not defined\n";
-        errOut << "SOLUTION: to activate the 2-pass mode, use --twopassMode Basic";
-        exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-    };
-
-
-
-    twoPass.yes=false;
-    if (twoPass.mode!="None") {//2-pass parameters
-        if (runMode!="alignReads")
-        {
-            ostringstream errOut;
-            errOut << "EXITING because of fatal PARAMETERS error: 2-pass mapping option  can only be used with --runMode alignReads\n";
-            errOut << "SOLUTION: remove --twopassMode option";
-            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-        };
-
-        if (twoPass.mode!="Basic")
-        {
-            ostringstream errOut;
-            errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --twopassMode="<<twoPass.mode<<"\n";
-            errOut << "SOLUTION: for the 2-pass mode, use allowed values --twopassMode: Basic";
-            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-        };
-
-        if (twoPass.pass1readsN==0)
-        {
-            ostringstream errOut;
-            errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN = 0 in the 2-pass mode\n";
-            errOut << "SOLUTION: for the 2-pass mode, specify --twopass1readsN > 0. Use a very large number or -1 to map all reads in the 1st pass.\n";
-            exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-        };
-
-        if (pGe.gLoad!="NoSharedMemory") {
-            ostringstream errOut;
-            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;
-        twoPass.dir=outFileNamePrefix+"_STARpass1/";
-        sysRemoveDir (twoPass.dir);
-        if (mkdir (twoPass.dir.c_str(),runDirPerm)!=0) {
-            ostringstream errOut;
-            errOut <<"EXITING because of fatal ERROR: could not make pass1 directory: "<< twoPass.dir<<"\n";
-            errOut <<"SOLUTION: please check the path and writing permissions \n";
-            exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-        };
-    };
-
    //sjdb insert on the fly
 
     sjdbInsert.pass1=false;

source/ParametersChimeric.h

@@ -13,6 +13,8 @@ class ParametersChimeric
         
         uint multimapScoreRange, multimapNmax, nonchimScoreDropMin;
         
+        vector<int> outJunctionFormat;
+
         struct
         {
             vector <string> stringIn;