Fixed a problem in STARsolo with empty Unmapped.out.mate2 file. Issue #…

…593.
alexdobin · Mar 22, 2019 · a3c2a09 · a3c2a09
1 parent bb207df
commit a3c2a09
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Showing 11 changed files with 2,983 additions and 2,975 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,4 @@
+* Fixed a problem in STARsolo with empty Unmapped.out.mate2 file. Issue #593.
 * Fixed a problem with CR CY UR UQ SAM tags in solo output. Issue #593.
 * Fixed problems with STARsolo and 2-pass.
 

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/ReadAlignChunk.cpp b/source/ReadAlignChunk.cpp
@@ -79,7 +79,7 @@ ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome
     };
     if (P.outReadsUnmapped=="Fastx" ) {
         chunkFstreamOpen(P.outFileTmp + "/Unmapped.out.mate1.thread",iChunk, RA->chunkOutUnmappedReadsStream[0]);
-        if (P.readNmates==2) chunkFstreamOpen(P.outFileTmp + "/Unmapped.out.mate2.thread",iChunk, RA->chunkOutUnmappedReadsStream[1]);
+        if (P.readNmatesIn==2) chunkFstreamOpen(P.outFileTmp + "/Unmapped.out.mate2.thread",iChunk, RA->chunkOutUnmappedReadsStream[1]);
     };
     if (P.outFilterType=="BySJout") {
         chunkFstreamOpen(P.outFileTmp + "/FilterBySJoutFiles.mate1.thread",iChunk, RA->chunkOutFilterBySJoutFiles[0]);

diff --git a/source/ReadAlignChunk_processChunks.cpp b/source/ReadAlignChunk_processChunks.cpp
@@ -232,7 +232,7 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks
             if (P.runThreadN>1)
                 pthread_mutex_lock(&g_threadChunks.mutexOutUnmappedFastx);
 
-            for (uint ii=0;ii<P.readNmates;ii++) {
+            for (uint ii=0;ii<P.readNmatesIn;ii++) {
                 chunkFstreamCat (RA->chunkOutUnmappedReadsStream[ii],P.inOut->outUnmappedReadsStream[ii], false, g_threadChunks.mutexOutUnmappedFastx);
             };
 

diff --git a/source/ReadAlign_outputAlignments.cpp b/source/ReadAlign_outputAlignments.cpp
@@ -219,6 +219,12 @@ void ReadAlign::outputAlignments() {
                 chunkOutUnmappedReadsStream[im] << Qual0[im] <<"\n";
             };
        };
+       if (P.pSolo.type>0) {//need to output 2nd (barcode) read
+           chunkOutUnmappedReadsStream[1] << readNameMates[0] <<"\n";
+           uint32 qualStart = readNameExtra[0].find(' ');
+           chunkOutUnmappedReadsStream[1] << readNameExtra[0].substr(0,qualStart) <<"\n+\n";
+           chunkOutUnmappedReadsStream[1] << readNameExtra[0].substr(qualStart+1) <<"\n";
+       };
     };
 };
 

diff --git a/source/VERSION b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.0e_0320"
+#define STAR_VERSION "2.7.0e_0322"
diff --git a/source/parametersDefault b/source/parametersDefault
@@ -1,6 +1,6 @@
 ### versions
 versionGenome           2.7.0d
-    string: latest genome index version compatible with this STAR release. Please do not change this value!
+    string: earliest genome index version compatible with this STAR release. Please do not change this value!
 
 ### Parameter Files
 parametersFiles          -

diff --git a/source/parametersDefault.xxd b/source/parametersDefault.xxd