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package driver;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
/** One-off program for converting grch38 sam files to hg19 */
public class FixChr {
public static void main(String[] args){
String in=args[0];
String out=args[1];
TextFile tf=new TextFile(in);
TextStreamWriter tsw=new TextStreamWriter(out, true, false, true);
tsw.start();
String s=null;
while((s=tf.nextLine())!=null){
if(!s.startsWith("#")){s="chr"+s;}
else if(s.startsWith("##contig=<ID=")){
s="##contig=<ID=chr"+s.substring("##contig=<ID=".length());
}
tsw.println(s);
}
tf.close();
tsw.poisonAndWait();
}
}
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