638 			int leftMax=leftCounts[leftMaxPos];  in processContigLeft()  local
646 				if(count>0 && isJunction(leftMax, count)){  in processContigLeft()
713 				final int leftMax=leftCounts[leftMaxPos];  in exploreRight()  local
716 				if(isJunction(leftMax, leftSecond)){  in exploreRight()
942 		int leftMax=minCountExtend;  in extendToRight()  local
948 			leftMax=leftCounts[leftMaxPos];  in extendToRight()
962 			outstream.println("leftMax="+leftMax);  in extendToRight()
973 …println("B: Breaking because isJunction("+rightMax+", "+rightSecond+", "+leftMax+", "+leftSecond+"…  in extendToRight()
974 			return isJunction(leftMax, leftSecond) ? D_BRANCH : F_BRANCH;  in extendToRight()
976 …if(isJunction(leftMax, leftSecond)){//Returning here is necessary, but this should mean the the le…  in extendToRight()
977 			assert(bb.length()==k) : bb.length()+", "+k+", "+leftMax+", "+leftSecond;  in extendToRight()
978 …println("B: Breaking because isJunction("+rightMax+", "+rightSecond+", "+leftMax+", "+leftSecond+"…  in extendToRight()
1016 				leftMax=leftCounts[leftMaxPos];  in extendToRight()
1030 				outstream.println("leftMax="+leftMax);  in extendToRight()
1040 			final boolean bbranch=isJunction(leftMax, leftSecond);  in extendToRight()
1043 …tream.println("B: Breaking - isJunction("+rightMax+", "+rightSecond+", "+leftMax+", "+leftSecond+"…  in extendToRight()
1048 						+ ""+leftMax+", "+leftSecond+"); ("+fbranch+", "+bbranch+", "+hbranch+")");}  in extendToRight()
1050 …"\nleftMaxPos="+leftMaxPos+", leftMax="+leftMax+", leftSecondPos="+leftSecondPos+", leftSecond="+l…  in extendToRight()
1075 …tream.println("B: Breaking - isJunction("+rightMax+", "+rightSecond+", "+leftMax+", "+leftSecond+"…  in extendToRight()
1144 		int leftMax=minCountExtend;  in extendToRight2()  local
1150 			leftMax=leftCounts[leftMaxPos];  in extendToRight2()
1173 		if(isJunction(rightMax, rightSecond, leftMax, leftSecond)){  in extendToRight2()
1174 ….println("Returning because isJunction: "+rightMax+", "+rightSecond+"; "+leftMax+", "+leftSecond);}  in extendToRight2()
1203 				leftMax=leftCounts[leftMaxPos];  in extendToRight2()
1222 			if(isJunction(rightMax, rightSecond, leftMax, leftSecond)){  in extendToRight2()
1223 …println("B: Breaking because isJunction("+rightMax+", "+rightSecond+", "+leftMax+", "+leftSecond+"…  in extendToRight2()
1233 …"\nleftMaxPos="+leftMaxPos+", leftMax="+leftMax+", leftSecondPos="+leftSecondPos+", leftSecond="+l…  in extendToRight2()