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package structures;
import java.util.ArrayList;
import shared.KillSwitch;
import shared.Parse;
import shared.Tools;
import stream.Read;
public class Quantizer {
public static boolean parse(String arg, String a, String b){
if(a.equals("quantize")){
if(b!=null && b.equalsIgnoreCase("sticky")){
STICKY=true;
return true;
}
}else if(a.equals("quantizesticky")){
if(b!=null && (b.charAt(0)=='/' || Tools.isDigit(b.charAt(0)))) {
STICKY=true;
}else {
STICKY=Parse.parseBoolean(b);
return true;
}
}
if(b==null || b.length()<1 || Character.isLetter(b.charAt(0))){
return Parse.parseBoolean(b);
}
return setArray(b);
}
private static boolean setArray(String s){
final byte[] array;
if(s.indexOf(',')<0){
if(s.charAt(0)=='/') {s=s.substring(1);}
int quant=Integer.parseInt(s);
assert(quant>0 && quant<128);
if(quant==1){return false;}
ByteBuilder bb=new ByteBuilder();
for(int i=0, max=Read.MAX_CALLED_QUALITY(); i<=max; i+=quant){
bb.append((byte)i);
}
array=bb.toBytes();
}else{
array=Parse.parseByteArray(s, ",");
}
setArray(array);
return true;
}
private static void setArray(byte[] a){
quantizeArray=a;
qualityRemapArray=makeQualityRemapArray(quantizeArray);
}
public static void quantize(ArrayList<Read> list) {
if(list==null) {return;}
for(Read r : list) {
if(r!=null) {
quantize(r);
quantize(r.mate);
}
}
}
public static void quantize(Read r1, Read r2){
quantize(r1);
quantize(r2);
}
public static void quantize(Read r){
if(r!=null) {quantize(r.quality);}
}
public static void quantize(byte[] quals){
if(quals==null){return;}
byte prev=0;
for(int i=0; i<quals.length; i++){
final byte qOld=quals[i];
final byte q0=qualityRemapArray[qOld];
byte q=q0;
if(STICKY && q!=prev && prev>0 && q>0 && Tools.absdif(qOld, prev)<=Tools.absdif(qOld, q)){q=prev;}
// assert(q==q0) : STICKY+", "+qOld+" -> "+q0+" -> "+q+", prev="+prev;
quals[i]=q;
prev=q;
}
}
private static final byte[] makeQualityRemapArray(byte[] quantizeArray) {
byte[] array=KillSwitch.allocByte1D(128);
for(int i=0; i<array.length; i++){
byte q=0;
for(byte x : quantizeArray){
if((i>0 && q==0 && x>0) || Tools.absdif(x, i)<=Tools.absdif(q, i)){q=x;}
}
array[i]=q;
}
return array;
}
// private static byte[] quantizeArray={0, 8, 13, 22, 27, 32, 37}; //Old
private static byte[] quantizeArray={0, 14, 21, 27, 32, 36};
private static byte[] qualityRemapArray=makeQualityRemapArray(quantizeArray);
private static boolean STICKY=true;
}
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