CHANGES.md

+STAR 2.6.1c 2018/10/17
+======================
+
+* Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.
+
 STAR 2.6.1b 2018/09/06
 ======================
 

source/ReadAlign_chimericDetectionPEmerged.cpp

@@ -39,7 +39,7 @@ void ReadAlign::chimericDetectionPEmerged(ReadAlign &seRA) {
                 };
             };
             for (uint jj=0; jj<2; jj++) {
-                if (segLen[ii][jj]<segLmin) {
+                if (segLen[ii][jj]<segLmin || (segLen[ii][jj]==segLmin && trChim[ii].exons[0][EX_G]>trChim[ii-1].exons[0][EX_G])) {
                     segLmin=segLen[ii][jj];
                     i1=ii;//trChim of the shortest segment length
                     i2=jj;//mate of the shortest segment length

source/SequenceFuns.cpp

@@ -139,7 +139,7 @@ void convertNucleotidesToNumbers(const char* R0, char* R1, const uint Lread) {//
                         case (84): case(116): 
                             R1[jj]=char(3);break;//T
                         default:                              
-                            R1[jj]=char(9);//anything else
+                            R1[jj]=char(4);//anything else is converted to N
                     };
                 };
 };
@@ -160,7 +160,7 @@ uint convertNucleotidesToNumbersRemoveControls(const char* R0, char* R1, const u
                 if (int(R0[jj]) < 32) {//control characters are skipped
                     continue;
                 } else {//all non-control non-ACGT characters are convreted to N
-                    R1[jj]=char(9);//anything else
+                    R1[jj]=char(4);//anything else
                 };
         };
         ++iR1;

source/VERSION

-#define STAR_VERSION "STAR_2.6.1b"
+#define STAR_VERSION "STAR_2.6.1c"

source/readLoad.cpp

@@ -84,7 +84,7 @@ int readLoad(istream& readInStream, Parameters& P, uint iMate, uint& Lread, uint
     } else {
         Lread=0;
     };
-    convertNucleotidesToNumbers(Seq+P.clip5pNbases[iMate],SeqNum,Lread);
+    convertNucleotidesToNumbersRemoveControls(Seq+P.clip5pNbases[iMate],SeqNum,Lread);
 
     //clip the adapter
     if (P.clip3pAdapterSeq.at(iMate).length()>0) {