2.7.10b_alpha_23-06-09: Issue #1871: Fixed a bug which occurs when --…

…soloCellReadStats Standard --twopassMode Basic are used together.
alexdobin · Jun 9, 2023 · 56c9fd5 · 56c9fd5
1 parent 45fe3dd
commit 56c9fd5
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/source/ReadAlign_outputAlignments.cpp b/source/ReadAlign_outputAlignments.cpp
@@ -5,9 +5,6 @@
 void ReadAlign::outputAlignments() {
 
     outBAMbytes=0;
-
-    if (P.pSolo.readStats.yes)
-        soloRead->readFlagReset();
 
     readAnnot.reset();
 

diff --git a/source/SoloRead_record.cpp b/source/SoloRead_record.cpp
@@ -7,6 +7,9 @@ void SoloRead::record(uint64 nTr, Transcript **alignOut, uint64 iRead, ReadAnnot
     if (pSolo.type==pSolo.SoloTypes::CB_samTagOut)
         return;
 
+    if (pSolo.readStats.yes)
+        readFlagReset();
+
     for (uint32 ii=0; ii<pSolo.nFeatures; ii++)
         readFeat[ii]->record(*readBar, nTr, alignOut, iRead, readAnnot);
 };
diff --git a/source/VERSION b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.10b_alpha_230301"
+#define STAR_VERSION "2.7.10b_alpha_23-06-09"
diff --git a/source/twoPassRunPass1.cpp b/source/twoPassRunPass1.cpp
@@ -43,7 +43,8 @@ void twoPassRunPass1(Parameters &P, Genome &genomeMain, Transcriptome *transcrip
 
     P1.wasp.outputMode="None"; //no WASP filtering on the 1st pass
     P1.pSolo.type=P1.pSolo.SoloTypes::None; //no solo in the first pass
-
+    P1.pSolo.yes = false;
+
     g_statsAll.resetN();
     time(&g_statsAll.timeStartMap);
     P.inOut->logProgress << timeMonthDayTime(g_statsAll.timeStartMap) <<"\tStarted 1st pass mapping\n" <<flush;