Array Index Out of bounds?

Code :

]public static int[] encode(int array[]) throws FileNotCompressedException 
	{
	    int[] count=new int[array.length];
		int[] Tarray=new int[array.length];
		int j=0;
		int c=0;
		int NewArray[]=new int[array.length];
		System.out.println(array[2]);
		for (int i=0; i<array.length; i++)
		{	
			if(array[i]==array[i+1])
			{
				if(count[j]==0)
				{
					count[j]++;
				}
				count[j]++;
			}
			else
			{
				Tarray[c]=array[i];
				c++;
				j++;
 
				if(count[j]==0)
				{
					count[j]++;
				}
 
			}
 
		}
		if(count.length+Tarray.length>=array.length)
		{
 
			throw new FileNotCompressedException();
		}
		else
		{	int a=0;
			int k=0;
			while(a<NewArray.length)
			{	
 
				NewArray[a]=count[k];
				NewArray[a+1]=Tarray[k];
				a=a+2;
				k++;
			}
			return NewArray;
		}
 
 
	}

This is a small part of my code but to keep it short, i read from a file that has 1000's of int then i need to sort them in a special way but when i use my for loop to begin my sort i get that error on array[i]=array[i+1]; that says array index out of bounds but when i print array[1000] or any other it works fine;