diff --git a/CHANGES.md b/CHANGES.md index e8b2af65..ed480043 100644 --- 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 deleted file mode 100755 index 95969427..00000000 Binary files a/bin/Linux_x86_64/STAR and /dev/null differ diff --git a/bin/Linux_x86_64/STARlong b/bin/Linux_x86_64/STARlong deleted file mode 100755 index 734804f2..00000000 Binary files a/bin/Linux_x86_64/STARlong and /dev/null differ diff --git a/bin/Linux_x86_64_static/STAR b/bin/Linux_x86_64_static/STAR deleted file mode 100755 index 1ab06677..00000000 Binary files a/bin/Linux_x86_64_static/STAR and /dev/null differ diff --git a/bin/Linux_x86_64_static/STARlong b/bin/Linux_x86_64_static/STARlong deleted file mode 100755 index 2b7e138b..00000000 Binary files a/bin/Linux_x86_64_static/STARlong and /dev/null differ diff --git a/bin/MacOSX_x86_64/STAR b/bin/MacOSX_x86_64/STAR deleted file mode 100755 index 904f112f..00000000 Binary files a/bin/MacOSX_x86_64/STAR and /dev/null differ diff --git a/bin/MacOSX_x86_64/STARlong b/bin/MacOSX_x86_64/STARlong deleted file mode 100755 index 017aa480..00000000 Binary files a/bin/MacOSX_x86_64/STARlong and /dev/null differ diff --git a/source/ReadAnnotations.h b/source/ReadAnnotations.h index 86f251c1..afb8d91e 100644 --- a/source/ReadAnnotations.h +++ b/source/ReadAnnotations.h @@ -10,7 +10,7 @@ class ReadAnnotFeature {//annotations for one feature set fSet; //set of genes for this read vector> 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 index 0e223800..2355ec9c 100644 --- a/source/Transcriptome_alignExonOverlap.cpp +++ b/source/Transcriptome_alignExonOverlap.cpp @@ -21,7 +21,7 @@ void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandTyp //vGeStrOvAl.reserve(256); //TODO: check if this affects speed - typedef array OverlapTypes; + typedef array OverlapTypes; struct GeneInfo1 { uint32 g; uint32 ia; @@ -29,7 +29,7 @@ void Transcriptome::alignExonOverlap(uint nA, Transcript **aAll, int32 strandTyp }; vector 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 index 83319541..61028e79 100644 --- a/source/VERSION +++ b/source/VERSION @@ -1 +1 @@ -#define STAR_VERSION "2.7.10b" +#define STAR_VERSION "2.7.10b_alpha_220111"