quick-tested: plugged some memory leaks

rlink.cpp

@@ -9,10 +9,8 @@ extern FILE *c_out;         // file handle for the input transcripts that are fu
 
 extern bool specific;
 extern bool trim;
-extern bool partialcov;
+//extern bool partialcov;
 extern bool complete;
-//extern bool debugMode;
-//extern bool verbose;
 extern bool eonly;
 
 extern int maxReadCov;
@@ -7781,15 +7779,15 @@ int build_graphs(BundleData* bdata, bool fast) {
 
 	//if(guides.Count()) fprintf(stderr,"No of guides=%d partialcov=%d\n",guides.Count(),partialcov);
 
-	if(partialcov) {
+	/* if(partialcov) {
 		for(int g=0;g<guides.Count();g++) {
 			int s=0;
 			if(guides[g]->strand=='+') s=2;
 			get_partial_covered(guides[g],bundle[s],bnode[s],junction);
 		}
 		return(0);
 	}
-
+    */
 	if(c_out || (bundle[1].Count() && bnode[1].Count())) // coverage is needed
 		for(int g=0;g<guides.Count();g++) {
 			//fprintf(stderr,"consider guide %d\n",g);

rlink.h

@@ -52,10 +52,8 @@ struct GRefData {
             GError("Error: invalid genomic sequence data (%s)!\n",gseq_name);
         rnas.setCapacity(gffr->gseqStats[gseq_id]->fcount);
      }
-     //int tidx=
      rnas.Add(t);
      t->isUsed(true);
-     //t->udata=tidx;
   }
 
   bool operator==(GRefData& d){
@@ -337,7 +335,7 @@ struct BundleData {
  void rc_init(GffObj* t) {
 	  if (rc_data==NULL) {
 	  	rc_data = new RC_BundleData(t->start, t->end);
-	    }
+	  }
  }
  /* after reference annotation was loaded
  void rc_finalize_refs() {

stringtie.cpp

@@ -87,7 +87,7 @@ bool fast=true;
 bool eonly=false; // parameter -e
 bool specific=false;
 bool complete=true;
-bool partialcov=false;
+//bool partialcov=false;
 int num_cpus=1;
 int mintranscriptlen=200; // minimum length for a transcript to be printed
 int sensitivitylevel=1;
@@ -375,11 +375,11 @@ if (ballgown)
 			 /*if (guides && ng_end>=ng_start) {
 				 for (int gi=ng_start;gi<=ng_end;gi++) {
 					 int tidx=bundle->keepguides.Add((*guides)[gi]);
-					 (*guides)[gi]->udata=tidx; //tid when not ballgown
+					 (*guides)[gi]->udata=tidx+1; //tid when not ballgown
 				 }
 			 }*/
 			// geneno=infer_transcripts(geneno, lastref, $label,\@readlist,$readthr,
-			 // \@junction,$junctionthr,$mintranscriptlen,\@keepguides);
+			// \@junction,$junctionthr,$mintranscriptlen,\@keepguides);
 			// (readthr, junctionthr, mintranscriptlen are globals)
 			bundle->getReady(currentstart, currentend);
 #ifndef NOTHREADS
@@ -521,9 +521,10 @@ if (ballgown)
 			 } while (cend_changed);
 		 }
 	 } //adjusted currentend and checked for overlapping reference transcripts
-     bool ref_overlap=false;
+      //bool ref_overlap=false;
 	 //if (ballgown && bundle->rc_data)
-      ref_overlap=bundle->evalReadAln(*brec, xstrand, nh);
+      //ref_overlap=
+      bundle->evalReadAln(*brec, xstrand, nh);
       if (xstrand=='+') strand=1;
 		else if (xstrand=='-') strand=-1;
 	  countFragment(*bundle, *brec, hi);
@@ -567,8 +568,7 @@ if (ballgown)
 
  //if (f_out && f_out!=stdout) fclose(f_out);
  fclose(f_out);
-
- // write the FPKMs
+ if (c_out && c_out!=stdout) fclose(c_out);
 
  if(verbose) {
 	 GMessage("Total count of aligned fragments: %llu\n",Num_Fragments);
@@ -581,6 +581,7 @@ if (ballgown)
 	 f_out=fopen(outfname.chars(), "w");
 	 if (f_out==NULL) GError("Error creating output file %s\n", outfname.chars());
  }
+
  fprintf(f_out,"# ");
  args.printCmdLine(f_out);
  fprintf(f_out,"# StringTie version %s\n",VERSION);
@@ -804,22 +805,21 @@ GStr Process_Options(GArgs* args) {
 	 if (ballgown && !guided)
 		 GError("Error: invalid -B/-b usage, GFF reference not given (-G option required).\n");
 
-	 s=args->getOpt('P');
+	 /* s=args->getOpt('P');
 	 if (!s.is_empty()) {
 		 if(!guided) GError("Error: option -G with reference annotation file has to be specified.\n");
 		 c_out=fopen(s.chars(), "w");
 		 if (c_out==NULL) GError("Error creating output file %s\n", s.chars());
 		 partialcov=true;
 	 }
-	 else {
+	 else { */
 		 s=args->getOpt('C');
 		 if (!s.is_empty()) {
 			 if(!guided) GError("Error: invalid -C usage, GFF reference not given (-G option required).\n");
 			 c_out=fopen(s.chars(), "w");
 			 if (c_out==NULL) GError("Error creating output file %s\n", s.chars());
-			 num_cpus=1;
 		 }
-	 }
+	 //}
 
 	 int numbam=args->startNonOpt();
 	 if (numbam==0 || numbam>1) {
@@ -891,7 +891,7 @@ void processBundle(BundleData* bundle) {
 #endif
 	}
 	int ngenes=infer_transcripts(bundle, fast | bundle->covSaturated);
-	if (bundle->rc_data) {
+	if (ballgown && bundle->rc_data) {
 		rc_update_exons(*(bundle->rc_data));
 	}
 	if (bundle->pred.Count()>0) {

tablemaker.cpp

@@ -29,7 +29,7 @@ void BundleData::keepGuide(GffObj* t) {
 	if (rc_data==NULL) {
 	  rc_init(t);
 	}
-	t->udata=keepguides.Add(t);
+	t->udata=keepguides.Add(t)+1;
 	rc_data->addTranscript(*t);
 }
 
@@ -40,7 +40,6 @@ struct COvlSorter {
   }
 } OvlSorter;
 
-
 void rc_updateExonCounts(const RC_Feature* exon, int nh) {
   exon->rcount++;
   exon->mrcount += (nh > 1) ? (1.0/nh) : 1;

tablemaker.h

@@ -232,7 +232,12 @@ struct RC_BundleData {
 	 exons(true, false, true), introns(true, false, true),
 	 xcache(0), xcache_pos(0)
 	 {
-	 if (rmax>lmin && ballgown) updateCovSpan();
+	 if (ballgown) {
+		 if (rmax>lmin) updateCovSpan();
+	 }else {
+		 exons.setFreeItem(true);
+		 introns.setFreeItem(true);
+	 }
  }
 
  ~RC_BundleData() {