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package hiseq;
import java.util.Arrays;
import dna.AminoAcid;
import shared.Tools;
import stream.Read;
/**
* Tracks base and quality composition per cycle.
*
* @author Brian Bushnell
* @date August 16, 2018
*
*/
public class CycleTracker {
public void add(Read r){
if(r==null || r.length()<1){return;}
addBases(r.bases);
addQuality(r.quality);
}
public void add(CycleTracker ct){
// assert(false) : length+", "+ct.length;
final long[][] matrix=ct.acgtnq;
if(matrix[0]==null){return;}
if(acgtnq[0]==null || ct.length>length){
resize(ct.length);
}
for(int i=0; i<matrix.length; i++){
for(int j=0; j<matrix[i].length; j++){
acgtnq[i][j]+=matrix[i][j];
}
}
}
//Do this before using results
public void process(){
// System.err.println("Processing); length="+length);
if(length<1){return;}
long[] cycleSum=new long[length];
for(int i=0; i<5; i++){
long[] array=acgtnq[i];
for(int j=0; j<array.length; j++){
cycleSum[j]+=array[j];
}
}
maxes=new float[6];
averages=new float[6];
for(int i=0; i<6; i++){
cycleAverages[i]=new float[length];
long[] array=acgtnq[i];
for(int j=0; j<length; j++){
float f=array[j]/(float)cycleSum[j];
cycleAverages[i][j]=f;
maxes[i]=Tools.max(f, maxes[i]);
}
}
long[] sum=new long[6];
long sumsum=0;
for(int i=0; i<5; i++){
long x=shared.Vector.sum(acgtnq[i]);
sum[i]=x;
sumsum+=x;
}
sum[5]=shared.Vector.sum(acgtnq[5]);
for(int i=0; i<6; i++){
averages[i]=sum[i]/(float)sumsum;
}
}
/*--------------------------------------------------------------*/
private void addBases(byte[] bases){
if(length<bases.length){resize(bases.length);}
for(int i=0; i<bases.length; i++){
byte b=bases[i];
int x=AminoAcid.baseToNumberACGTN[b];
assert(x>=0) : "This program does not support degenerate base codes: "+new String(bases);
acgtnq[x][i]++;
}
}
private void addQuality(byte[] quals){
if(quals==null){return;}
if(length<quals.length){resize(quals.length);}
final long[] sum=acgtnq[5];
for(int i=0; i<quals.length; i++){
byte q=quals[i];
sum[i]+=q;
}
}
private void resize(int newLen){
assert(newLen>length);
length=newLen;
if(acgtnq[0]==null){
for(int i=0; i<acgtnq.length; i++){
acgtnq[i]=new long[newLen];
}
}else{
for(int i=0; i<acgtnq.length; i++){
acgtnq[i]=Arrays.copyOf(acgtnq[i], newLen);
}
}
}
public float max(byte base) {
final int x=AminoAcid.baseToNumberACGTN[base];
return(maxes[x]);
}
public float max(char base) {
final int x=AminoAcid.baseToNumberACGTN[base];
return(maxes[x]);
}
public float avg(byte base) {
final int x=AminoAcid.baseToNumberACGTN[base];
return(averages[x]);
}
public float avg(char base) {
final int x=AminoAcid.baseToNumberACGTN[base];
return(averages[x]);
}
public void clear() {
for(long[] array : acgtnq) {Arrays.fill(array, 0);}
for(float[] array : cycleAverages) {Arrays.fill(array, 0);}
Arrays.fill(maxes, 0);
Arrays.fill(averages, 0);
}
/*--------------------------------------------------------------*/
public long[][] acgtnq=new long[6][];
public float[][] cycleAverages=new float[6][];
public float[] maxes;
public float[] averages;
public int length=0;
}
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