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package driver;
import java.util.HashSet;
import fileIO.TextFile;
import shared.Tools;
import stream.SamLine;
public class TrimSamFile {
public static void main(String[] args){
String fname=args[0];
String scaf=args[1];
int from=Integer.parseInt(args[2]);
int to=Integer.parseInt(args[3]);
TextFile tf=new TextFile(fname, false);
HashSet<String> set=findBadLines(tf, scaf, from, to);
tf.reset();
printExcludingSet(tf, set);
}
public static HashSet<String> findBadLines(TextFile tf, String scafS, int from, int to){
byte[] scaf=scafS.getBytes();
HashSet<String> set=new HashSet<String>(16000);
for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(s.charAt(0)!='@'){//header
SamLine sl=new SamLine(s);
if(sl.pos>=from && sl.pos<=to && Tools.equals(sl.rname(), scaf)){
set.add(sl.qname);
}else if(sl.pnext>=from && sl.pnext<=to && Tools.equals(sl.rnext(), scaf)){
set.add(sl.qname);
}else if(Tools.equals(sl.rname(), scaf) && Tools.equals(sl.rnext(), scaf) && (sl.pos<from != sl.pnext<from)){
set.add(sl.qname);
}else if(!sl.mapped() || !sl.nextMapped() || !sl.pairedOnSameChrom()){
set.add(sl.qname);
}
}
}
return set;
}
public static void printExcludingSet(TextFile tf, HashSet<String> set){
for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(s.charAt(0)=='@'){//header
System.out.println(s);
}else{
SamLine sl=new SamLine(s);
if(!set.contains(sl.qname)){
System.out.println(s);
}
}
}
}
}
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