From c2f3c6589ffab7c69fc46684b5be0990584b7542 Mon Sep 17 00:00:00 2001
From: Alexander Dobin <dobin@cshl.edu>
Date: Wed, 1 Jun 2022 14:05:01 -0400
Subject: [PATCH] Bug-fix alpha: 2.7.10a_alpha_220601 : Issue #1543: Fixed a
 segfault occurring for STARsolo multimappers and large number of reads per
 cell.

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

diff --git a/CHANGES.md b/CHANGES.md
index 396861dc..b16f7e98 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,4 @@
+* Issue #1543: Fixed a segfault occurring for STARsolo multimappers and large number of reads per cell.
 * 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.
diff --git a/source/SoloFeature_collapseUMIall_multiMappers.cpp b/source/SoloFeature_collapseUMIall_multiMappers.cpp
index 9023bbd7..269142a8 100644
--- a/source/SoloFeature_collapseUMIall_multiMappers.cpp
+++ b/source/SoloFeature_collapseUMIall_multiMappers.cpp
@@ -17,8 +17,8 @@ void SoloFeature::collapseUMIall(uint32 iCB, uint32 *umiArray)
 
     uint32 gid1 = -1;//current gID
     uint32 nGenes = 0, nGenesMult = 0; //number of genes
-    uint32 *gID = new uint32[min(featuresNumber,rN)+1]; //gene IDs
-    uint32 *gReadS = new uint32[min(featuresNumber,rN)+1]; //start of gene reads TODO: allocate this array in the 2nd half of rGU
+    uint32 *gID = new uint32[min(2*featuresNumber,rN)+1]; //gene IDs, 2* is needed because each gene can have unique and multi-mappers
+    uint32 *gReadS = new uint32[min(2*featuresNumber,rN)+1]; //start of gene reads TODO: allocate this array in the 2nd half of rGU
     for (uint32 iR=0; iR<rN*rguStride; iR+=rguStride) {
         if (rGU[iR+rguG]!=gid1) {//record gene boundary
             gReadS[nGenes]=iR;
diff --git a/source/VERSION b/source/VERSION
index 5a641f07..80514cf4 100644
--- a/source/VERSION
+++ b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.10a_alpha_220517"
+#define STAR_VERSION "2.7.10a_alpha_220601"