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package driver;
import fileIO.TextFile;
import shared.Tools;
/**
* For BBMerge comparison data collation
* @author Brian Bushnell
* @date Mar 15, 2016
*
*/
public class ProcessFragMerging {
public static void main(String[] args){
String sym="\t";
String fname=args[0];
TextFile tf=new TextFile(fname);
for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
String[] split=line.split("\\p{javaWhitespace}+");
if(line.startsWith("***")){
System.out.print("\n"+split[1]+sym);
// System.out.println("\n"+line);
}else if(line.startsWith("real")){
String time=line.split("\t")[1];
double seconds=toSeconds(time);
System.out.print(Tools.format("%.3f", seconds)+sym);
}else if(line.startsWith("Reads Used:")){
System.out.print(split[2]+sym+split[3].substring(1)+sym);
}else if(line.startsWith("mapped:")){
System.out.print(split[2]+sym+split[4]+sym);
}else if(line.startsWith("Error Rate:")){
System.out.print(split[3]+sym+split[5]+sym);
}else if(line.startsWith("Sub Rate:")){
System.out.print(split[3]+sym+split[5]+sym);
}else if(line.startsWith("Del Rate:")){
System.out.print(split[3]+sym+split[5]+sym);
}else if(line.startsWith("Ins Rate:")){
System.out.print(split[3]+sym+split[5]+sym);
}
// Del Rate: 0.0161% 168 0.0276% 64385
// Ins Rate: 0.0017% 18 0.0002% 366
}
}
public static double toSeconds(String s){
s=s.replaceAll("s", "");
String[] split=s.split("m");
String seconds=split[1], minutes=split[0];
return 60*Double.parseDouble(minutes)+Double.parseDouble(seconds);
}
}
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