Finalizing STARdiploid.

source/ReadAlign_alignBAM.cpp

@@ -365,6 +365,14 @@ int ReadAlign::alignBAM(Transcript const &trOut, uint nTrOut, uint iTrOut, uint
                         break;
                     };
 
+                    case ATTR_ha:
+                    {
+                        if (mapGen.pGe.transform.type==2) {
+                            attrN+=bamAttrArrayWrite( (int32) trOut.haploType, "ha", attrOutArray+attrN );
+                        };
+                        break; 
+                    };
+
                     case ATTR_ch:
                         if (alignType<=-10)
                         {//chimeric alignment

source/ReadAlign_multMapSelect.cpp

@@ -53,6 +53,8 @@ void ReadAlign::multMapSelect() {//select multiple mappers from all transcripts
         trMult[iTr]->cStart=trMult[iTr]->gStart - mapGen.chrStart[trMult[iTr]->Chr];
     };
 
+
+    //TODO: use funPrimaryAlignMark
     if (nTr==1){//unique mappers
         trMult[0]->primaryFlag=true;
     } else {//multimappers
@@ -91,4 +93,3 @@ void ReadAlign::multMapSelect() {//select multiple mappers from all transcripts
 
     //TODO re-point trBest to the primary one. This should not make a difference in the output
 };
-

source/funPrimaryAlignFlag.cpp

@@ -0,0 +1,39 @@
+void funPrimaryAlignMark(Transcript **trMult, uint64 nTr, Parameters &P)
+{
+    if (nTr==1){//unique mappers
+        trMult[0]->primaryFlag=true;
+    } else {//multimappers
+        int nbest=0;
+        if (P.outMultimapperOrder.random || P.outSAMmultNmax != (uint) -1 ) {//bring the best alignment to the top of the list. TODO sort alignments by the score?
+            for (uint itr=0; itr<nTr; itr++) {//move the best aligns to the top of the list
+                if ( trMult[itr]->maxScore == maxScore ) {
+                    swap(trMult[itr],trMult[nbest]);
+                    ++nbest;
+                };
+            };
+        };
+
+        if (P.outMultimapperOrder.random) {//shuffle separately the best aligns, and the rest
+            for (int itr=nbest-1; itr>=1; itr--) {//Fisher-Yates-Durstenfeld-Knuth shuffle
+                int rand1=int (rngUniformReal0to1(rngMultOrder)*itr+0.5);
+                swap(trMult[itr],trMult[rand1]);
+            };
+            for (int itr=nTr-nbest-1; itr>=1; itr--) {//Fisher-Yates-Durstenfeld-Knuth shuffle
+                int rand1=int (rngUniformReal0to1(rngMultOrder)*itr+0.5);
+                swap(trMult[nbest+itr],trMult[nbest+rand1]);
+            };
+        };
+
+        if ( P.outSAMprimaryFlag=="AllBestScore" ) {
+            for (uint itr=0; itr<nTr; itr++)
+            {//mark all best score aligns as primary
+                if ( trMult[itr]->maxScore == maxScore ) trMult[itr]->primaryFlag=true;
+            };
+        } else if (P.outMultimapperOrder.random || P.outSAMmultNmax != (uint) -1) {
+            trMult[0]->primaryFlag=true;//mark as primary the first one in the random ordered list: best scoring aligns are already in front of the list
+        } else {//old way
+            trBest->primaryFlag=true;
+        };
+    };
+};
+