patchfix release 2.2.2

Author: gpertea

gclib/GBase.h

@@ -249,9 +249,10 @@ inline void GFree(pointer* ptr){
 
 inline bool GMalloc(pointer* ptr,unsigned long size){
     //GASSERT(ptr);
+    *ptr=nullptr;
     if (size!=0)
   	  *ptr=malloc(size);
-    return *ptr!=NULL;
+    return *ptr!=nullptr;
  }
 
 // Allocate 0-filled memory

gclib/GSam.h

@@ -248,8 +248,7 @@ class GSamRecord: public GSeg {
         p = bam_get_qname(b);
 
         strcpy(p,qname.c_str());
-        uint16_t x = 0;
-
+        
         for (int x=l;x<l+l_extranul;x++){
             p[x] = '\0';
         }

rlink.cpp

@@ -16320,7 +16320,7 @@ void merge_exons(CGene& gene,GVec<GSeg>& exons) {
 
 void update_overlap(GList<CPrediction>& pred,int p,int e,GVec<CExon>& node,OvlTracker& overlaps) {
 
-	int n=pred.Count();
+	//int n=pred.Count();
 	for(int i=0;i<node.Count();i++) if(!overlaps.get(node[i].predno, p)) { // there is no overlap detected yet
 
 		// exon e in prediction p overlaps exon ei in prediction pi

stringtie.cpp

@@ -464,11 +464,11 @@ if (ballgown)
 #define DEF_TSTACK_SIZE 8388608
  size_t defStackSize=DEF_TSTACK_SIZE;
 #ifdef _GTHREADS_POSIX_
- int tstackSize=GThread::defaultStackSize();
+ size_t tstackSize=GThread::defaultStackSize();
  if (tstackSize<DEF_TSTACK_SIZE) defStackSize=DEF_TSTACK_SIZE;
  if (verbose) {
    if (tstackSize<defStackSize){
-    int ssize=defStackSize;
+    size_t ssize=defStackSize;
     GMessage("Default stack size for threads: %d (increased to %d)\n", tstackSize, ssize);
    }
    else GMessage("Default stack size for threads: %d\n", tstackSize);