Fixed a bug with causing seg-faults when combining --twopassMode Basi…

…c --outSAMorder PairedKeepInputOrder .
wososa · May 25, 2016 · a7756f5 · a7756f5
1 parent 487b836
commit a7756f5
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Showing 7 changed files with 9 additions and 2 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,4 @@
+* Fixed a bug with causing seg-faults when combining  --twopassMode Basic --outSAMorder PairedKeepInputOrder .
 * Fixed a problem with SAM header in cases where reference sequences are added at the mapping stage.
 
 STAR 2.5.2a 2016/05/10

diff --git a/bin/Linux_x86_64/STAR b/bin/Linux_x86_64/STAR
diff --git a/bin/Linux_x86_64/STARlong b/bin/Linux_x86_64/STARlong
diff --git a/bin/Linux_x86_64_static/STAR b/bin/Linux_x86_64_static/STAR
diff --git a/bin/Linux_x86_64_static/STARlong b/bin/Linux_x86_64_static/STARlong
diff --git a/source/Parameters.cpp b/source/Parameters.cpp
@@ -624,9 +624,15 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
     if (outFilterType=="BySJout" && outSAMorder=="PairedKeepInputOrder") {
         ostringstream errOut;
         errOut <<"EXITING: fatal input ERROR: --outFilterType=BySJout is not presently compatible with --outSAMorder=PairedKeepInputOrder\n";
-        errOut <<"SOLUTION: re-run STAR without setting one of those parameters. Send a feature request to the Authors\n";
+        errOut <<"SOLUTION: re-run STAR without setting one of those parameters.\n";
         exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
     };
+    if (!outSAMbool && outSAMorder=="PairedKeepInputOrder") {
+        ostringstream errOut;
+        errOut <<"EXITING: fatal input ERROR: --outSAMorder=PairedKeepInputOrder is presently only compatible with SAM output, i.e. default --outSMAtype SAM\n";
+        errOut <<"SOLUTION: re-run STAR without --outSAMorder=PairedKeepInputOrder, or with --outSAMorder=PairedKeepInputOrder --outSMAtype SAM .\n";
+        exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+    };    
     //SJ filtering
     for (int ii=0;ii<4;ii++) {
         if (outSJfilterOverhangMin.at(ii)<0) outSJfilterOverhangMin.at(ii)=numeric_limits<int32>::max();

diff --git a/source/ReadAlignChunk_mapChunk.cpp b/source/ReadAlignChunk_mapChunk.cpp
@@ -89,7 +89,7 @@ void ReadAlignChunk::mapChunk() {//map one chunk. Input reads stream has to be s
 
     }; //reads cycle
 
-    if ( P->outSAMorder == "PairedKeepInputOrder" && P->runThreadN>1 ) {//write the remaining part of the buffer, close and rename chunk files
+    if ( P->outSAMbool && P->outSAMorder == "PairedKeepInputOrder" && P->runThreadN>1 ) {//write the remaining part of the buffer, close and rename chunk files
         chunkOutBAMfile.write(chunkOutBAM,chunkOutBAMtotal);
         chunkOutBAMfile.clear(); //in case 0 bytes were written which could set fail bit
         chunkOutBAMfile.close();