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package cluster;
import java.util.Arrays;
import java.util.concurrent.atomic.AtomicLongArray;
import dna.AminoAcid;
import jgi.Dedupe;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Mar 24, 2014
*
*/
public class ClusterTools {
public static int[] toKmerCounts(byte[] bases, Object object, int k) {
// TODO Auto-generated method stub
return null;
}
public static int[] toKmers(final byte[] bases, int[] array_, final int k){
if(bases==null || bases.length<k){return null;}
final int alen=bases.length-k+1;
final int[] array=(array_!=null && array_.length==alen ? array_ : new int[alen]);
final int shift=2*k;
final int shift2=shift-2;
final int mask=~((-1)<<shift);
int kmer=0;
int rkmer=0;
int len=0;
for(int i=0, j=0; i<bases.length; i++){
byte b=bases[i];
int x=Dedupe.baseToNumber[b];
int x2=Dedupe.baseToComplementNumber[b];
kmer=((kmer<<2)|x)&mask;
rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
// if(b=='N'){len=0; rkmer=0;}else{len++;} //This version will transform 'N' into 'A'
if(verbose){System.err.println("Scanning2 i="+i+", kmer="+kmer+", rkmer="+rkmer+", bases="+new String(bases, Tools.max(0, i-k), Tools.min(i+1, k)));}
if(len>=k){
array[j]=Tools.min(kmer, rkmer);
j++;
}
}
Arrays.sort(array);
return array;
}
public static int[] toKmerCounts(final byte[] bases, int[] array_, final int k, final int alen){
if(bases==null || bases.length<k){return null;}
final int[] array=(array_!=null && array_.length==alen ? array_ : new int[alen]);
final int shift=2*k;
final int shift2=shift-2;
final int mask=~((-1)<<shift);
int kmer=0;
int rkmer=0;
int len=0;
for(int i=0, j=0; i<bases.length; i++){
byte b=bases[i];
int x=Dedupe.baseToNumber[b];
int x2=Dedupe.baseToComplementNumber[b];
kmer=((kmer<<2)|x)&mask;
rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
// if(b=='N'){len=0; rkmer=0;}else{len++;} //This version will transform 'N' into 'A'
if(verbose){System.err.println("Scanning2 i="+i+", kmer="+kmer+", rkmer="+rkmer+", bases="+new String(bases, Tools.max(0, i-k), Tools.min(i+1, k)));}
if(len>=k){
array[Tools.min(kmer, rkmer)]++;
}
}
Arrays.sort(array);
return array;
}
public static int maxCanonicalKmer(int k){
final int bits=2*k;
final int max=(int)((1L<<bits)-1);
int high=0;
for(int kmer=0; kmer<=max; kmer++){
int canon=Tools.min(kmer, AminoAcid.reverseComplementBinaryFast(kmer, k));
high=Tools.max(canon, high);
}
return high;
}
/**
* @param kmers Read kmers
* @param counts Cluster kmer counts
* @return Score
*/
static final float andCount(int[] kmers, AtomicLongArray counts){
int sum=0;
for(int i=0; i<kmers.length; i++){
int kmer=kmers[i];
long count=counts.get(kmer);
if(count>0){sum++;}
}
return sum/(float)kmers.length;
}
/**
* @param kmers Read kmers
* @param probs Cluster kmer frequencies
* @return Score
*/
static final float innerProduct(int[] kmers, float[] probs){
float sum=0;
for(int kmer : kmers){
if(kmer>=0){
sum+=probs[kmer];
}
}
return sum;
}
/**
* @param a Read kmer frequencies
* @param b Cluster kmer frequencies
* @return Score
*/
static final float absDif(float[] a, float[] b){
assert(a.length==b.length);
double sum=0;
for(int i=0; i<a.length; i++){
sum+=Tools.absdif((double)a[i], (double)b[i]);
}
return (float)sum;
}
/**
* @param a Read kmer frequencies
* @param b Cluster kmer frequencies
* @return Score
*/
static final float rmsDif(float[] a, float[] b){
assert(a.length==b.length);
double sum=0;
for(int i=0; i<a.length; i++){
// double d=Tools.absdif((double)a[i], (double)b[i]);
double d=((double)a[i])-((double)b[i]);
sum+=d*d;
}
return (float)Math.sqrt(sum/a.length);
}
/**
* @param a Read kmer frequencies
* @param b Cluster kmer frequencies
* @return Score
*/
static final float ksFunction(float[] a, float[] b){
assert(a.length==b.length);
double sum=0;
for(int i=0; i<a.length; i++){
double ai=a[i]+0.00001;
double bi=b[i]+0.00001;
double d=(double)ai*Math.log(ai/bi);
sum+=d;
}
return (float)sum;
}
public static boolean verbose=false;
}
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