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package jgi;
import shared.Timer;
import stream.Read;
import stream.SamLine;
import template.BBTool_ST;
/**
* Changes quality scores to other quality scores.
* @author Brian Bushnell
* @date Apr 27, 2015
*
*/
public class RemapQuality extends BBTool_ST {
/**
* Code entrance from the command line.
* Must be overridden; the commented body is an example.
* @param args Command line arguments
*/
public static void main(String[] args){
//Example:
Timer t=new Timer();
RemapQuality bbt=new RemapQuality(args);
bbt.process(t);
}
@Override
protected void setDefaults(){}
/**
* @param args
*/
public RemapQuality(String[] args) {
super(args);
SamLine.SET_FROM_OK=true;
map=new byte[256];
for(int i=0; i<map.length; i++){
map[i]=(byte)i;
}
if(mapString==null){//reverse quality
for(int i=2; i<=41; i++){
map[i]=(byte)(43-i);
}
}else{
String[] pairs=mapString.split(";");
for(String pair : pairs){
String[] split=pair.split(",");
int a=Integer.parseInt(split[0]);
int b=Integer.parseInt(split[1]);
map[a]=(byte)b;
}
}
}
/* (non-Javadoc)
* @see jgi.BBTool_ST#parseArgument(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean parseArgument(String arg, String a, String b){
if(a.equals("map")){
mapString=b;
return true;
}else if(false){
return true;
}
return false;
}
/* (non-Javadoc)
* @see jgi.BBTool_ST#startupSubclass()
*/
@Override
protected void startupSubclass() {
// TODO Auto-generated method stub
}
/* (non-Javadoc)
* @see jgi.BBTool_ST#shutdownSubclass()
*/
@Override
protected void shutdownSubclass() {
// TODO Auto-generated method stub
}
/* (non-Javadoc)
* @see jgi.BBTool_ST#showStatsSubclass(dna.Timer, long, long)
*/
@Override
protected void showStatsSubclass(Timer t, long readsIn, long basesIn) {
// TODO Auto-generated method stub
}
@Override
protected final boolean useSharedHeader(){return true;}
/* (non-Javadoc)
* @see jgi.BBTool_ST#processReadPair(stream.Read, stream.Read)
*/
@Override
protected boolean processReadPair(Read r1, Read r2) {
if(r1!=null && r1.quality!=null){
final byte[] qual=r1.quality;
for(int i=0; i<qual.length; i++){qual[i]=map[qual[i]];}
}
if(r2!=null && r2.quality!=null){
final byte[] qual=r2.quality;
for(int i=0; i<qual.length; i++){qual[i]=map[qual[i]];}
}
return true;
}
public String mapString;
public final byte[] map;
}
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