From 56c9fd59d0cbddd630f9ed2a656dd3a963a1b6b4 Mon Sep 17 00:00:00 2001
From: Alexander Dobin <dobin@cshl.edu>
Date: Fri, 9 Jun 2023 13:11:39 -0400
Subject: [PATCH] 2.7.10b_alpha_23-06-09: Issue #1871: Fixed a bug which occurs
 when --soloCellReadStats Standard --twopassMode Basic are used together.

---
 source/ReadAlign_outputAlignments.cpp | 3 ---
 source/SoloRead_record.cpp            | 3 +++
 source/VERSION                        | 2 +-
 source/twoPassRunPass1.cpp            | 3 ++-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/source/ReadAlign_outputAlignments.cpp b/source/ReadAlign_outputAlignments.cpp
index 754ce2da..2cd6488a 100755
--- 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
index 6386ef47..17fec9e0 100755
--- 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
index 45f35583..468f82d2 100644
--- 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
index 5ebf545b..d8c28e15 100644
--- 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;