From 45fe3dd0a74048b40a91dd58f8f008e66dae3b58 Mon Sep 17 00:00:00 2001
From: Alexander Dobin <dobin@cshl.edu>
Date: Wed, 1 Mar 2023 12:55:59 -0500
Subject: [PATCH] 2.7.10b_alpha_230301: Issue #1763: Fixed a bug causing
 segnmentation fault in rare cases for 2-pass mapping.

---
 CHANGES.md                   | 1 +
 source/ReadAlign.cpp         | 7 +++++++
 source/ReadAlign.h           | 4 ++++
 source/ReadAlign_oneRead.cpp | 7 +++++++
 source/VERSION               | 2 +-
 source/sjdbBuildIndex.cpp    | 4 ++--
 6 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index ed480043..96d8c9f7 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,4 @@
+* Issue #1763: Fixed a bug causing segnmentation fault in rare cases for 2-pass mapping.
 * Issue #1733: Fixed the issue with counting of intronicAS reads in STARsolo CellReads.stats output with --soloFeatures GeneFull_Ex50pAS option.
 
 STAR 2.7.10b --- 2022/11/01 ::: Bug-fix release.
diff --git a/source/ReadAlign.cpp b/source/ReadAlign.cpp
index e2a8a3c8..44dd1d4d 100755
--- a/source/ReadAlign.cpp
+++ b/source/ReadAlign.cpp
@@ -101,6 +101,13 @@ ReadAlign::ReadAlign (Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, in
     
     //clipping
     P.pClip.initializeClipMates(clipMates);
+
+    //debug
+    {
+    #ifdef DEBUG_OutputLastRead
+        lastReadStream.open((P.outFileTmp+"/lastRead_"+to_string(iChunk)).c_str());
+    #endif
+    };
 };
 
 void ReadAlign::resetN () {//reset resets the counters to 0 for a new read
diff --git a/source/ReadAlign.h b/source/ReadAlign.h
index 7fcba404..452b6cbf 100755
--- a/source/ReadAlign.h
+++ b/source/ReadAlign.h
@@ -177,6 +177,10 @@ class ReadAlign {
         //read annotations
         ReadAnnotations readAnnot;
 
+        #ifdef DEBUG_OutputLastRead
+            ofstream lastReadStream;
+        #endif
+
         /////////////////////////////////////////////////////////////////// METHODS
         void resetN();//resets the counters to 0
         void multMapSelect();
diff --git a/source/ReadAlign_oneRead.cpp b/source/ReadAlign_oneRead.cpp
index 92d644ef..90b902e1 100755
--- a/source/ReadAlign_oneRead.cpp
+++ b/source/ReadAlign_oneRead.cpp
@@ -110,6 +110,13 @@ int ReadAlign::oneRead() {//process one read: load, map, write
     //write out alignments
     outputAlignments();
 
+    {
+    #ifdef DEBUG_OutputLastRead
+        lastReadStream.seekp(ios::beg);
+        lastReadStream << iReadAll <<" "<< readName <<endl;
+    #endif
+    };
+
     return 0;
 
 };
diff --git a/source/VERSION b/source/VERSION
index 61028e79..45f35583 100644
--- a/source/VERSION
+++ b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.10b_alpha_220111"
+#define STAR_VERSION "2.7.10b_alpha_230301"
diff --git a/source/sjdbBuildIndex.cpp b/source/sjdbBuildIndex.cpp
index 805dee96..4095f962 100644
--- a/source/sjdbBuildIndex.cpp
+++ b/source/sjdbBuildIndex.cpp
@@ -161,7 +161,7 @@ void sjdbBuildIndex (Parameters &P, char *Gsj, char *G, PackedArray &SA, PackedA
         if ( (ind1 & N2bit)>0 )
         {//- strand
             uint ind1s = mapGen1.nGenome - (ind1 & strandMask);
-            if (ind1s>mapGen.chrStart[mapGen.nChrReal])
+            if (ind1s>=mapGen.chrStart[mapGen.nChrReal])
             {//this index was an old sj, may need to shift it
                 uint sj1 = (ind1s-mapGen.chrStart[mapGen.nChrReal])/mapGen.sjdbLength;//old junction index
                 ind1s += (oldSJind[sj1]-sj1)*mapGen.sjdbLength;
@@ -172,7 +172,7 @@ void sjdbBuildIndex (Parameters &P, char *Gsj, char *G, PackedArray &SA, PackedA
             };
         } else
         {//+ strand
-            if (ind1>mapGen.chrStart[mapGen.nChrReal])
+            if (ind1>=mapGen.chrStart[mapGen.nChrReal])
             {//this index was an old sj, may need to shift it
                 uint sj1 = (ind1-mapGen.chrStart[mapGen.nChrReal])/mapGen.sjdbLength;//old junction index
                 ind1 += (oldSJind[sj1]-sj1)*mapGen.sjdbLength;