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package bloom;
/**
* @author Brian Bushnell
* @date Dec 2, 2014
*
*/
public abstract class KmerCountAbstract {
protected static final long[] transformToFrequency(int[] count){
long[] freq=new long[2000];
int max=freq.length-1;
for(int i=0; i<count.length; i++){
int x=count[i];
x=min(x, max);
freq[x]++;
}
return freq;
}
protected static final long sum(int[] array){
long x=0;
for(int y : array){x+=y;}
return x;
}
protected static final long sum(long[] array){
long x=0;
for(long y : array){x+=y;}
return x;
}
protected static final int min(int x, int y){return x<y ? x : y;}
protected static final int max(int x, int y){return x>y ? x : y;}
public static byte minQuality=6;
public static long readsProcessed=0;
public static long maxReads=-1;
public static float minProb=0.5f;
public static long keysCounted=0;
public static long increments=0;
public static final boolean verbose=false;
public static boolean PREJOIN=false;
public static boolean CANONICAL=false;
public static boolean KEEP_DUPLICATE_KMERS=true;
public static int KMERS_PER_READ=0;
public static int IDMASK=0;
public static int MAX_COUNT_THREADS=1024;
public static boolean SKETCH_MODE=false;
public static boolean STORE_HASHED=false;
public static boolean BUFFERED=false;
public static int BUFFERLEN=3000; //Optimal is in the range of 2000-8000 for Clumpified 2x150bp data.
// public static boolean SORT_SERIAL=false; //Not needed, see parallel sort flag
public static int maxShortKmerLength=31;
}
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