jpayne@68: package bloom;
jpayne@68: 
jpayne@68: import shared.Shared;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Dec 2, 2014
jpayne@68:  *
jpayne@68:  */
jpayne@68: public abstract class KmerCountAbstract {
jpayne@68: 
jpayne@68: 	protected static final long[] transformToFrequency(int[] count){
jpayne@68: 		long[] freq=new long[2000];
jpayne@68: 		int max=freq.length-1;
jpayne@68: 		for(int i=0; i<count.length; i++){
jpayne@68: 			int x=count[i];
jpayne@68: 			x=min(x, max);
jpayne@68: 			freq[x]++;
jpayne@68: 		}
jpayne@68: 		return freq;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	protected static final long sum(int[] array){
jpayne@68: 		long x=0;
jpayne@68: 		for(int y : array){x+=y;}
jpayne@68: 		return x;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	protected static final long sum(long[] array){
jpayne@68: 		long x=0;
jpayne@68: 		for(long y : array){x+=y;}
jpayne@68: 		return x;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	protected static final int min(int x, int y){return x<y ? x : y;}
jpayne@68: 	protected static final int max(int x, int y){return x>y ? x : y;}
jpayne@68: 	
jpayne@68: 	public static byte minQuality=6;
jpayne@68: 	public static long readsProcessed=0;
jpayne@68: 	public static long maxReads=-1;
jpayne@68: 	
jpayne@68: 	public static float minProb=0.5f;
jpayne@68: 
jpayne@68: 	public static long keysCounted=0;
jpayne@68: 	public static long increments=0;
jpayne@68: 	
jpayne@68: 	public static final boolean verbose=false;
jpayne@68: 	public static boolean PREJOIN=false;
jpayne@68: 	public static boolean CANONICAL=false;
jpayne@68: 	public static boolean KEEP_DUPLICATE_KMERS=true;
jpayne@68: 	public static boolean SKETCH_MODE=false;
jpayne@68: 	public static boolean STORE_HASHED=false;
jpayne@68: 	public static boolean BUFFERED=false;
jpayne@68: 	public static int BUFFERLEN=3000; //Optimal is in the range of 2000-8000 for Clumpified 2x150bp data.
jpayne@68: //	public static boolean SORT_SERIAL=false; //Not needed, see parallel sort flag
jpayne@68: 	
jpayne@68: 	public static int maxShortKmerLength=31;
jpayne@68: 	
jpayne@68: }