2.7.10b_alpha_220111: Issue #1733: Fixed the issue with counting of i…

…ntronicAS reads in STARsolo CellReads.stats output with --soloFeatures GeneFull_Ex50pAS option.
alexdobin · Jan 11, 2023 · f4fa8e8 · f4fa8e8
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,5 @@
+* 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.
 ===========================================================================
 * PR #1638: Increased entropy of shmKey to avoid collisions between genomes. Many thanks to Jeff Hussmann (@jeffhussmann).

diff --git a/bin/Linux_x86_64/STAR b/bin/Linux_x86_64/STAR
diff --git a/bin/Linux_x86_64/STARlong b/bin/Linux_x86_64/STARlong
diff --git a/bin/Linux_x86_64_static/STAR b/bin/Linux_x86_64_static/STAR
diff --git a/bin/Linux_x86_64_static/STARlong b/bin/Linux_x86_64_static/STARlong
diff --git a/bin/MacOSX_x86_64/STAR b/bin/MacOSX_x86_64/STAR
diff --git a/bin/MacOSX_x86_64/STARlong b/bin/MacOSX_x86_64/STARlong
diff --git a/source/ReadAnnotations.h b/source/ReadAnnotations.h
@@ -10,7 +10,7 @@ class ReadAnnotFeature {//annotations for one feature
     set<uint32> fSet;  //set of genes for this read
     vector<set<uint32>> fAlign; //gene for each alignment of this read
     uint32 ovType;
-    enum overlapTypes {none,exonic, exonicAS, intronic, intronicAS};
+    enum overlapTypes {none, exonic, exonicAS, intronic, intronicAS, N};
 
     void reset() {
         fSet={}; fAlign={}; ovType = 0;

diff --git a/source/Transcriptome_alignExonOverlap.cpp b/source/Transcriptome_alignExonOverlap.cpp
@@ -21,15 +21,15 @@ void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandTyp
     //vGeStrOvAl.reserve(256); //TODO: check if this affects speed
 
 
-    typedef array<bool,5> OverlapTypes;
+    typedef array<bool,6> OverlapTypes;
     struct GeneInfo1 {
         uint32 g;
         uint32 ia;
         OverlapTypes ot; //overlap types, prioritized
     };
     vector<GeneInfo1> vGeneInfo1;
     vGeneInfo1.reserve(256); //TODO: check if this affects speed
-    OverlapTypes otAS={false,true,false,true,false}; //which OverlapTypes is antisense, it will not be counted
+    OverlapTypes otAS={false,true,false,true,false,true}; //which OverlapTypes is antisense, it will not be counted
 
     /*//GeneFullClosest3p
     uint64 minDist3p=(uint64)-1;
@@ -86,6 +86,7 @@ void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandTyp
                                                             str1 && nOverlap>exl/2, 
                                                             !str1 && nOverlap>exl/2,
                                                             str1,
+                                                            !str1
                                                         } 
                                      });
 
@@ -207,8 +208,10 @@ void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandTyp
             annFeat.ovType = ReadAnnotFeature::overlapTypes::exonicAS;
         } else if (otFinal[4]) {
             annFeat.ovType = ReadAnnotFeature::overlapTypes::intronic;
-        } else {
+        } else if (otFinal[5]) {
             annFeat.ovType = ReadAnnotFeature::overlapTypes::intronicAS;
+        } else {
+            annFeat.ovType = ReadAnnotFeature::overlapTypes::none; //intergenic. i.e. no overlap with genes
         };
 
         // annFeat.fSet={};

diff --git a/source/VERSION b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "2.7.10b"
+#define STAR_VERSION "2.7.10b_alpha_220111"