CHANGES.md

+STAR 2.6.1b 2018/09/06
+======================
+
+* Fixed a problem with --outSAMfilter KeepOnlyAddedReferences option.
+* Fixed a problem with output of an empty sorted BAM.
+
+
 STAR 2.6.1a 2018/08/14
 ======================
 

debian/changelog

+rna-star (2.6.1b+dfsg-1) unstable; urgency=medium
+
+  * New upstream version.
+  * Bump Standards-Version.
+
+ -- Steffen Moeller <moeller@debian.org>  Tue, 18 Sep 2018 18:53:06 +0200
+
 rna-star (2.6.1a+dfsg-1) unstable; urgency=medium
 
   * New upstream release.

debian/control

@@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 11),
                libhts-dev,
                vim-common,
                zlib1g-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/rna-star
 Vcs-Git: https://salsa.debian.org/med-team/rna-star.git
 Homepage: https://github.com/alexdobin/STAR/

source/BAMoutput.cpp

@@ -127,7 +127,7 @@ void BAMoutput::coordBins() {//define genomic starts for bins
     if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexBAMsortBins);
     if (P.outBAMsortingBinStart[0]!=0) {//it's set to 0 only after the bin sizes are determined
         //extract coordinates and sort
-        uint *startPos = new uint [binTotalN[0]];//array of aligns start positions
+        uint *startPos = new uint [binTotalN[0]+1];//array of aligns start positions
         for (uint ib=0,ia=0;ia<binTotalN[0];ia++) {
             uint32 *bamIn32=(uint32*) (binStart[0]+ib);
             startPos[ia]  =( ((uint) bamIn32[1]) << 32) | ( (uint)bamIn32[2] );

source/Genome.cpp

@@ -336,10 +336,10 @@ void Genome::genomeLoad(){//allocate and load Genome
     else if (pGe.gLoad=="NoSharedMemory") // simply allocate memory, do not use shared memory
     {
         genomeInsertL=0;
+        genomeInsertChrIndFirst=nChrReal;
         if (pGe.gFastaFiles.at(0)!="-")
         {//will insert sequences in the genome, now estimate the extra size
            uint oldlen=chrStart.back();//record the old length
-           genomeInsertChrIndFirst=nChrReal;
            genomeInsertL=genomeScanFastaFiles(P, G, false, *this)-oldlen;
         };
 

source/Parameters.cpp

@@ -737,6 +737,14 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
         exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
     };
 
+    if ( (outSAMfilter.KeepOnlyAddedReferences || outSAMfilter.KeepAllAddedReferences) && pGe.gFastaFiles.at(0)=="-" ) {
+        ostringstream errOut;
+        errOut <<"EXITING because of FATAL INPUT ERROR: --outSAMfilter KeepOnlyAddedReferences OR KeepAllAddedReferences options can only be used if references are added on-the-fly with --genomeFastaFiles" <<"\n";
+        errOut <<"SOLUTION: use default --outSAMfilter None, OR add references with --genomeFataFiles\n";
+        exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+    };
+       
+    
     if (outMultimapperOrder.mode=="Old_2.4")
     {
         outMultimapperOrder.random=false;

source/STAR.cpp

@@ -403,11 +403,20 @@ int main(int argInN, char* argIn[]) {
             errOut <<"EXITING because of fatal ERROR: not enough memory for BAM sorting: \n";
             errOut <<"SOLUTION: re-run STAR with at least --limitBAMsortRAM " <<maxMem+1000000000;
             exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
+        } else if(maxMem==0) {
+            P.inOut->logMain << "WARNING: nothing to sort - no output alignments" <<endl;
+            BGZF *bgzfOut;
+            bgzfOut=bgzf_open(P.outBAMfileCoordName.c_str(),("w"+to_string((long long) P.outBAMcompression)).c_str());
+            if (bgzfOut==NULL) {
+                ostringstream errOut;
+                errOut <<"EXITING because of fatal ERROR: could not open output bam file: " << P.outBAMfileCoordName << "\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(bgzfOut,P.samHeaderSortedCoord,mainGenome.chrNameAll,mainGenome.chrLengthAll);
+            bgzf_close(bgzfOut);
+        } else {//sort
             uint totalMem=0;
-//         P.inOut->logMain << "Started sorting BAM ..." <<endl;
             #pragma omp parallel num_threads(P.outBAMsortingThreadNactual)
             #pragma omp for schedule (dynamic,1)
             for (uint32 ibin1=0; ibin1<nBins; ibin1++) {
@@ -439,6 +448,7 @@ int main(int argInN, char* argIn[]) {
                     totalMem-=newMem;//"release" RAM
                 };
             };
+        
             //concatenate all BAM files, using bam_cat
             char **bamBinNames = new char* [nBins];
             vector <string> bamBinNamesV;
@@ -455,6 +465,7 @@ int main(int argInN, char* argIn[]) {
             };
             bam_cat(bamBinNamesV.size(), bamBinNames, 0, P.outBAMfileCoordName.c_str());
         };
+    };
     //wiggle output
     if (P.outWigFlags.yes) {
         *(P.inOut->logStdOut) << timeMonthDayTime() << " ..... started wiggle output\n" <<flush;

source/VERSION

-#define STAR_VERSION "STAR_2.6.1a"
+#define STAR_VERSION "STAR_2.6.1b"