reverted a049f69 for a proper fix

Author: gpertea

bundle.h

@@ -398,6 +398,7 @@ struct BundleData {
 	pred.Clear();
 	pred.setSorted(false);
 	readlist.Clear();
+	readlist.setSorted(false);
 	for(int i=0;i<3;i++) {
 		bpcov[i].Clear();
 		bpcov[i].setCapacity(1024);

rlink.cpp

@@ -1673,28 +1673,20 @@ int add_read_to_group(int n,GList<CReadAln>& readlist,int color,GPVec<CGroup>& g
 				int readcol=usedcol[sno];
 
 				if(np<n) { // there is a pair and it came before the current read in sorted order of position
-					// first group of pair read is: readgroup[np][0] -- but only if readgroup[np] is not empty
-					if (readgroup[np].Count() > 0) {
-						int grouppair=readgroup[np][0];
-						while( merge[grouppair]!=grouppair) {
-							grouppair=merge[grouppair];
-						}
-						readgroup[np][0]=grouppair;
+					// first group of pair read is: readgroup[np][0]
 
-						readcol=group[readgroup[np][0]]->color;    // readcol gets assigned the color of the pair's first group --> this might not
-																	// work if I split  a read into multiple groups
-						while(eqcol[readcol]!=readcol) { // get smallest color
-							readcol=eqcol[readcol];
-						}
-						group[readgroup[np][0]]->color=readcol;
-					} else { // missing previous entry?
-						if (readcol < 0) {
-								usedcol[sno] = color;
-								readcol = color;
-								eqcol.Add(color);
-								++color;
-						}
+					int grouppair=readgroup[np][0];
+					while( merge[grouppair]!=grouppair) {
+						grouppair=merge[grouppair];
+					}
+					readgroup[np][0]=grouppair;
+
+					readcol=group[readgroup[np][0]]->color;    // readcol gets assigned the color of the pair's first group --> this might not
+															   // work if I split  a read into multiple groups
+					while(eqcol[readcol]!=readcol) { // get smallest color
+						readcol=eqcol[readcol];
 					}
+					group[readgroup[np][0]]->color=readcol;
 				}
 				else { // it's the first time I see the read in the fragment
 					//fragno+=readlist[n]->pair_count[p];