From 071e98967f4ca0e4b76936ddf9d73e98758d5792 Mon Sep 17 00:00:00 2001
From: Alexander Dobin <dobin@cshl.edu>
Date: Tue, 17 May 2022 13:16:17 -0400
Subject: [PATCH] Issue #1558: Fixed a bug with output of GX/GN BAM tags
 without CB/UB. Bug-fix alpha patch: 2.7.10a_alpha_220517

---
 CHANGES.md                | 1 +
 source/ParametersSolo.cpp | 3 ++-
 source/VERSION            | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 39d27fb8..396861dc 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,4 @@
+* Issue #1558: Fixed a bug with output of GX/GN BAM tags without CB/UB.
 * Fixed a bug with --soloMultiMappers for small number of cells cases.
 * Issue #1513: If --soloMultiMappers options are not requested, output "NoMulti" in the "Reads Mapped to Gene: Unique+Multiple Gene" line of the Summary.csv file.
 * Fixed a problem with STARsolo CellReads.stats output for no-passlist runs.
diff --git a/source/ParametersSolo.cpp b/source/ParametersSolo.cpp
index f2736f81..9fa4e48b 100755
--- a/source/ParametersSolo.cpp
+++ b/source/ParametersSolo.cpp
@@ -398,10 +398,11 @@ void ParametersSolo::initialize(Parameters *pPin)
     if (featureYes[SoloFeatureTypes::VelocytoSimple] || featureYes[SoloFeatureTypes::Velocyto]) {//turn readInfo on for Gene needed by VelocytoSimple
         readInfoYes[SoloFeatureTypes::Gene]=true;
     };
+    samAttrFeature = featureFirst;
     if (samAttrYes){//pSolo.samAttrFeature=0 by default, so need to check samAttrYes
         if (   featureFirst == SoloFeatureTypes::Gene || featureFirst == SoloFeatureTypes::GeneFull ||
                featureFirst == SoloFeatureTypes::GeneFull_Ex50pAS || featureFirst == SoloFeatureTypes::GeneFull_ExonOverIntron ) {
-            samAttrFeature = featureFirst;
+            //all good
         } else {
             ostringstream errOut;
             errOut << "EXITING because of fatal PARAMETERS error: CB and/or UB attributes in --outSAMattributes require --soloFeatures Gene OR/AND GeneFull OR/AND GeneFull_Ex50pAS.\n";
diff --git a/source/VERSION b/source/VERSION
index ff4a57eb..5a641f07 100644
--- a/source/VERSION
+++ b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.10a_alpha_220506"
+#define STAR_VERSION "2.7.10a_alpha_220517"