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package jgi;
import fileIO.ByteFile;
import fileIO.ByteStreamWriter;
import shared.Timer;
import shared.Tools;
import stream.SamLine;
public class SplitSamFile {
public static void main(String[] args){
Timer t=new Timer();
String in=args[0];
String outF=args.length>1 ? args[1] : null;
String outR=args.length>2 ? args[2] : null;
String outU=args.length>3 ? args[3] : null;
if(args.length>4){
if(args[4].equalsIgnoreCase("header")){includeHeader=true;}
}
ByteFile tf=ByteFile.makeByteFile(in, false);
Tools.testForDuplicateFiles(true, in, outF, outR, outU);
Tools.testOutputFiles(true, false, false, outF, outR, outU);
final ByteStreamWriter fStream, rStream, uStream;
fStream=(outF==null ? null : new ByteStreamWriter(outF, true, false, true));
rStream=(outR==null ? null : new ByteStreamWriter(outR, true, false, true));
uStream=(outU==null ? null : new ByteStreamWriter(outU, true, false, true));
if(fStream!=null){fStream.start();}
if(rStream!=null){rStream.start();}
if(uStream!=null){uStream.start();}
long plus=0;
long minus=0;
long other=0;
byte[] s=null;
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(s.length>0){
byte c=s[0];
if(c=='@'){
if(includeHeader){
if(fStream!=null){fStream.println(s);}
if(rStream!=null){rStream.println(s);}
if(uStream!=null){uStream.println(s);}
}
}else{
int flag=SamLine.parseFlagOnly(s);
if(SamLine.mapped(flag)){
if(SamLine.strand(flag)==0){
if(fStream!=null){fStream.println(s);}
plus++;
}else{
if(rStream!=null){rStream.println(s);}
minus++;
}
}else{
if(uStream!=null){uStream.println(s);}
other++;
}
}
}
}
tf.close();
if(fStream!=null){fStream.poisonAndWait();}
if(rStream!=null){rStream.poisonAndWait();}
if(uStream!=null){uStream.poisonAndWait();}
System.err.println("Total reads: \t"+(plus+minus+other));
System.err.println("Plus reads: \t"+(plus));
System.err.println("Minus reads: \t"+(minus));
System.err.println("Unmapped reads:\t"+(other));
t.stop();
System.err.println("Time: \t"+t);
}
private static boolean includeHeader=false;
}
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