From 5f9b2eab32e01e542121db93d88e35ba790a9013 Mon Sep 17 00:00:00 2001
From: HU Xuesong <87519979+huxs001@users.noreply.github.com>
Date: Sat, 24 Feb 2024 14:15:31 +0800
Subject: [PATCH] When `soloOutFormatFeaturesGeneField3` is `+`, write
 GeneBiotype as FeaturesGeneField3.

---
 source/SoloFeature_outputResults.cpp | 5 ++++-
 source/parametersDefault             | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/source/SoloFeature_outputResults.cpp b/source/SoloFeature_outputResults.cpp
index bf07c4cf..31d8c7ed 100644
--- a/source/SoloFeature_outputResults.cpp
+++ b/source/SoloFeature_outputResults.cpp
@@ -35,7 +35,10 @@ void SoloFeature::outputResults(bool cellFilterYes, string outputPrefixMat)
             for (uint32 ii=0; ii<Trans.nGe; ii++) {
                 geneStr << Trans.geID[ii] <<"\t"<< (Trans.geName[ii].empty() ? Trans.geID[ii] : Trans.geName[ii]);
                 if (pSolo.outFormat.featuresGeneField3!="-") {
-                    geneStr <<'\t'<< pSolo.outFormat.featuresGeneField3;
+                    if (pSolo.outFormat.featuresGeneField3 == "+")
+                        geneStr <<'\t'<< (Trans.geBiotype[ii].empty() ? "MissingGeneType" : Trans.geBiotype[ii]);
+                    else
+                        geneStr <<'\t'<< pSolo.outFormat.featuresGeneField3;
                 };
                 geneStr << '\n';
             };
diff --git a/source/parametersDefault b/source/parametersDefault
index 056222b8..9ba9f417 100755
--- a/source/parametersDefault
+++ b/source/parametersDefault
@@ -907,7 +907,7 @@ soloCellFilter              CellRanger2.2 3000 0.99 10
                                                 The harcoded values are from CellRanger:             3000            0.99            10    45000    90000      500               0.01      20000  0.01  10000
 
 soloOutFormatFeaturesGeneField3    "Gene Expression"
-    string(s):                field 3 in the Gene features.tsv file. If "-", then no 3rd field is output.
+    string(s):                field 3 in the Gene features.tsv file. If "+", then GeneBiotype is used. If "-", then no 3rd field is output.
 
 soloCellReadStats           None
     string:                 Output reads statistics for each CB