464 	int nextgr=0;  in get_min_start()  local
471 		    	nextgr = currgroup[twogr]->start < currgroup[2]->start ? twogr : 2;  in get_min_start()
472 		    	return(nextgr);  in get_min_start()
475 		    	nextgr = currgroup[0]->start < currgroup[1]->start ? 0 : 1;  in get_min_start()
476 		    	return(nextgr);  in get_min_start()
481 		    	nextgr = currgroup[0]->start < currgroup[2]->start ? 0 : 2;  in get_min_start()
482 		    	return(nextgr);  in get_min_start()
492 		    	nextgr = currgroup[1]->start < currgroup[2]->start ? 1 : 2;  in get_min_start()
493 		    	return(nextgr);  in get_min_start()
504 	return(nextgr);  in get_min_start()
11888 		int nextgr=get_min_start(currgroup); // gets the index of currgroup with the left most begining  in build_graphs()  local
11890 		int grcol = currgroup[nextgr]->color;    // set smallest color for currgroup[$nextgr]  in build_graphs()
11895 		currgroup[nextgr]->color=grcol;  in build_graphs()
11900 		if(nextgr == 1) { // unknown strand group  in build_graphs()
11902 …if(prevgroup[0]!=NULL && currgroup[nextgr]->start <= prevgroup[0]->end+bundledist) { // overlaps p…  in build_graphs()
11904 				set_strandcol(currgroup[nextgr],prevgroup[0],prevgroup[0]->color,eqnegcol,equalcolor);  in build_graphs()
11905 …uint maxstart = currgroup[nextgr]->start > prevgroup[0]->start ? currgroup[nextgr]->start : prevgr…  in build_graphs()
11906 …uint minend = currgroup[nextgr]->end < prevgroup[0]->end ? currgroup[nextgr]->end : prevgroup[0]->…  in build_graphs()
11908 				currgroup[nextgr]->neg_prop+=prevgroup[0]->cov_sum*(minend-maxstart+1)/prevgroup[0]->len();  in build_graphs()
11911 …currgroup[0]!=NULL && currgroup[nextgr]->start <= currgroup[0]->end+bundledist && currgroup[0]->st…  in build_graphs()
11921 				set_strandcol(currgroup[nextgr],currgroup[0],currgroup[0]->color,eqnegcol,equalcolor);  in build_graphs()
11922 …uint maxstart = currgroup[nextgr]->start > currgroup[0]->start ? currgroup[nextgr]->start : currgr…  in build_graphs()
11923 …uint minend = currgroup[nextgr]->end < currgroup[0]->end ? currgroup[nextgr]->end : currgroup[0]->…  in build_graphs()
11925 				currgroup[nextgr]->neg_prop+=currgroup[0]->cov_sum*(minend-maxstart+1)/currgroup[0]->len();  in build_graphs()
11933 …if(prevgroup[2]!=NULL && currgroup[nextgr]->start <= prevgroup[2]->end + bundledist) { // overlaps…  in build_graphs()
11935 				set_strandcol(currgroup[nextgr],prevgroup[2],prevgroup[2]->color,eqposcol,equalcolor);  in build_graphs()
11936 				if(currgroup[nextgr]->neg_prop) {  in build_graphs()
11937 …uint maxstart = currgroup[nextgr]->start > prevgroup[2]->start ? currgroup[nextgr]->start : prevgr…  in build_graphs()
11938 …uint minend = currgroup[nextgr]->end < prevgroup[2]->end ? currgroup[nextgr]->end : prevgroup[2]->…  in build_graphs()
11944 …urrgroup[2]!=NULL && currgroup[nextgr]->start <= currgroup[2]->end +bundledist && currgroup[2]->st…  in build_graphs()
11953 				set_strandcol(currgroup[nextgr],currgroup[2],currgroup[2]->color,eqposcol,equalcolor);  in build_graphs()
11954 				if(currgroup[nextgr]->neg_prop) {  in build_graphs()
11955 …uint maxstart = currgroup[nextgr]->start > currgroup[2]->start ? currgroup[nextgr]->start : currgr…  in build_graphs()
11956 …uint minend = currgroup[nextgr]->end < currgroup[2]->end ? currgroup[nextgr]->end : currgroup[2]->…  in build_graphs()
11966 				currgroup[nextgr]->neg_prop/=(currgroup[nextgr]->neg_prop+pos_prop);  in build_graphs()
11968 			else if(currgroup[nextgr]->neg_prop) currgroup[nextgr]->neg_prop=1;  in build_graphs()
11971 		else if(nextgr == 0) { // negative strand group  in build_graphs()
11972 			currgroup[nextgr]->neg_prop=1;  in build_graphs()
11976 		prevgroup[nextgr]=currgroup[nextgr];  in build_graphs()
11977 		currgroup[nextgr]=currgroup[nextgr]->next_gr;  in build_graphs()
12038 		int nextgr=get_min_start(currgroup);  // next group based on starting position  in build_graphs()  local
12041 		int grcol = currgroup[nextgr]->color;  in build_graphs()
12046 		currgroup[nextgr]->color=grcol;  in build_graphs()
12048 …if(nextgr == 0 || nextgr ==2 || (nextgr==1 &&(eqnegcol[grcol]==-1) && (eqposcol[grcol]==-1))) { //…  in build_graphs()
12054 				add_group_to_bundle(currgroup[nextgr],bundle[nextgr][bno],bnode[nextgr],bundledist);  in build_graphs()
12057 				bno=create_bundle(bundle[nextgr],currgroup[nextgr],bnode[nextgr]);  in build_graphs()
12062 			group2bundle[nextgr][currgroup[nextgr]->grid]=bundle[nextgr][bno]->lastnodeid;  in build_graphs()
12076 …add_group_to_bundle(currgroup[nextgr],bundle[0][bno],bnode[0],bundledist); // this needs bundledist  in build_graphs()
12079 					bno=create_bundle(bundle[0],currgroup[nextgr],bnode[0]);  in build_graphs()
12083 				group2bundle[0][currgroup[nextgr]->grid]=bundle[0][bno]->lastnodeid;  in build_graphs()
12096 					add_group_to_bundle(currgroup[nextgr],bundle[2][bno],bnode[2],bundledist);  in build_graphs()
12099 					bno=create_bundle(bundle[2],currgroup[nextgr],bnode[2]);  in build_graphs()
12104 				group2bundle[2][currgroup[nextgr]->grid]=bundle[2][bno]->lastnodeid;  in build_graphs()
12109 		currgroup[nextgr]=currgroup[nextgr]->next_gr;  in build_graphs()
12764 		int nextgr=get_min_start(currgroup); // gets the index of currgroup with the left most begining  in build_merge()  local
12766 		int grcol = currgroup[nextgr]->color;    // set smallest color for currgroup[$nextgr]  in build_merge()
12771 		currgroup[nextgr]->color=grcol;  in build_merge()
12774 		if(nextgr == 1) { // unknown strand group  in build_merge()
12777 …if(prevgroup[0]!=NULL && currgroup[nextgr]->start <= prevgroup[0]->end) { // overlaps previous neg…  in build_merge()
12779 				set_strandcol(currgroup[nextgr],prevgroup[0],prevgroup[0]->color,eqnegcol,equalcolor);  in build_merge()
12780 …uint maxstart = currgroup[nextgr]->start > prevgroup[0]->start ? currgroup[nextgr]->start : prevgr…  in build_merge()
12781 …uint minend = currgroup[nextgr]->end < prevgroup[0]->end ? currgroup[nextgr]->end : prevgroup[0]->…  in build_merge()
12782 				currgroup[nextgr]->neg_prop+=prevgroup[0]->cov_sum*(minend-maxstart+1)/prevgroup[0]->len();  in build_merge()
12786 …hile(currgroup[0]!=NULL && currgroup[nextgr]->start <= currgroup[0]->end && currgroup[0]->start <=…  in build_merge()
12795 				set_strandcol(currgroup[nextgr],currgroup[0],currgroup[0]->color,eqnegcol,equalcolor);  in build_merge()
12796 …uint maxstart = currgroup[nextgr]->start > currgroup[0]->start ? currgroup[nextgr]->start : currgr…  in build_merge()
12797 …uint minend = currgroup[nextgr]->end < currgroup[0]->end ? currgroup[nextgr]->end : currgroup[0]->…  in build_merge()
12798 				currgroup[nextgr]->neg_prop+=currgroup[0]->cov_sum*(minend-maxstart+1)/currgroup[0]->len();  in build_merge()
12807 …if(prevgroup[2]!=NULL && currgroup[nextgr]->start <= prevgroup[2]->end) { // overlaps positive str…  in build_merge()
12808 				set_strandcol(currgroup[nextgr],prevgroup[2],prevgroup[2]->color,eqposcol,equalcolor);  in build_merge()
12809 				if(currgroup[nextgr]->neg_prop) {  in build_merge()
12810 …uint maxstart = currgroup[nextgr]->start > prevgroup[2]->start ? currgroup[nextgr]->start : prevgr…  in build_merge()
12811 …uint minend = currgroup[nextgr]->end < prevgroup[2]->end ? currgroup[nextgr]->end : prevgroup[2]->…  in build_merge()
12817 …hile(currgroup[2]!=NULL && currgroup[nextgr]->start <= currgroup[2]->end && currgroup[2]->start <=…  in build_merge()
12825 				set_strandcol(currgroup[nextgr],currgroup[2],currgroup[2]->color,eqposcol,equalcolor);  in build_merge()
12826 				if(currgroup[nextgr]->neg_prop) {  in build_merge()
12827 …uint maxstart = currgroup[nextgr]->start > currgroup[2]->start ? currgroup[nextgr]->start : currgr…  in build_merge()
12828 …uint minend = currgroup[nextgr]->end < currgroup[2]->end ? currgroup[nextgr]->end : currgroup[2]->…  in build_merge()
12837 				currgroup[nextgr]->neg_prop/=(currgroup[nextgr]->neg_prop+pos_prop);  in build_merge()
12839 			else if(currgroup[nextgr]->neg_prop) currgroup[nextgr]->neg_prop=1;  in build_merge()
12842 		else if(nextgr == 0) { // negative strand group  in build_merge()
12843 			currgroup[nextgr]->neg_prop=1;  in build_merge()
12846 		prevgroup[nextgr]=currgroup[nextgr];  in build_merge()
12847 		currgroup[nextgr]=currgroup[nextgr]->next_gr;  in build_merge()
12908 		int nextgr=get_min_start(currgroup);  // next group based on starting position  in build_merge()  local
12911 		int grcol = currgroup[nextgr]->color;  in build_merge()
12916 		currgroup[nextgr]->color=grcol;  in build_merge()
12918 …if(nextgr == 0 || nextgr ==2 || (nextgr==1 &&(eqnegcol[grcol]==-1) && (eqposcol[grcol]==-1))) { //…  in build_merge()
12923 …add_group_to_bundle(currgroup[nextgr],bundle[nextgr][bno],bnode[nextgr],0); // last parameter was …  in build_merge()
12926 				bno=create_bundle(bundle[nextgr],currgroup[nextgr],bnode[nextgr]);  in build_merge()
12930 			group2bundle[nextgr][currgroup[nextgr]->grid]=bundle[nextgr][bno]->lastnodeid;  in build_merge()
12944 …add_group_to_bundle(currgroup[nextgr],bundle[0][bno],bnode[0],0); // last parameter was bundledist…  in build_merge()
12947 					bno=create_bundle(bundle[0],currgroup[nextgr],bnode[0]);  in build_merge()
12951 				group2bundle[0][currgroup[nextgr]->grid]=bundle[0][bno]->lastnodeid;  in build_merge()
12963 …add_group_to_bundle(currgroup[nextgr],bundle[2][bno],bnode[2],0); // last parameter was bundledist…  in build_merge()
12966 					bno=create_bundle(bundle[2],currgroup[nextgr],bnode[2]);  in build_merge()
12970 				group2bundle[2][currgroup[nextgr]->grid]=bundle[2][bno]->lastnodeid;  in build_merge()
12975 		currgroup[nextgr]=currgroup[nextgr]->next_gr;  in build_merge()