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package jgi;
import dna.AminoAcid;
import shared.Timer;
import stream.Read;
import template.BBTool_ST;
/**
* @author Brian Bushnell
* @date Mar 16, 2015
*
*/
public class RemoveBadBarcodes extends BBTool_ST {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
/**
* 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){
Timer t=new Timer();
RemoveBadBarcodes bbt=new RemoveBadBarcodes(args);
bbt.process(t);
}
/**
* @param args
*/
public RemoveBadBarcodes(String[] args) {
super(args);
}
@Override
protected void setDefaults(){}
@Override
public boolean parseArgument(String arg, String a, String b) {
return false;
}
@Override
protected boolean processReadPair(Read r1, Read r2) {
String id=r1.id;
int loc=(id==null ? -1 : id.lastIndexOf(':'));
if(loc<0 || loc>=id.length()-1){
noBarcode++;
return false;
}
for(int i=loc+1; i<id.length(); i++){
char c=id.charAt(i);
boolean ok=(c=='+' || AminoAcid.isFullyDefined(c));
if(!ok){
bad++;
return false;
}
}
good++;
return true;
}
@Override
protected void startupSubclass() {}
protected @Override
void shutdownSubclass() {}
@Override
protected final boolean useSharedHeader(){return true;}
@Override
protected void showStatsSubclass(Timer t, long readsIn, long basesIn) {
outstream.println();
outstream.println("Good: "+good);
outstream.println("Bad: "+bad);
outstream.println("No Barcode: "+noBarcode);
}
long good=0;
long bad=0;
long noBarcode=0;
}
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