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package jgi;
import java.io.PrintStream;
import fileIO.FileFormat;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.SamLine;
/**
* @author Brian Bushnell
* @date Jul 23, 2013
*
*/
public class SplitSam4Way {
public static void main(String[] args){
SplitSam4Way x=new SplitSam4Way(args);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
private void printOptions(){
outstream.println("Syntax:\n");
outstream.println("java -ea -Xmx128m -cp <path> jgi.SplitSam4Way <input> <out plus> <out minus> <out chimeric> <out unmapped>");
outstream.println("If you do not want one of the output files, use the word 'null'.\n");
}
public SplitSam4Way(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
if(args==null || args.length!=5){
printOptions();
System.exit(1);
}
Timer t=new Timer();
long reads=0, bases=0;
long preads=0, mreads=0, creads=0, ureads=0;
String fin=args[0];
String fplus=args[1];
String fminus=args[2];
String fchimeric=args[3];
String funmapped=args[4];
TextFile tf=new TextFile(fin, true);
TextStreamWriter plus=("null".equalsIgnoreCase(fplus) ? null : new TextStreamWriter(fplus, true, false, true, FileFormat.SAM));
TextStreamWriter minus=("null".equalsIgnoreCase(fminus) ? null : new TextStreamWriter(fminus, true, false, true, FileFormat.SAM));
TextStreamWriter chimeric=("null".equalsIgnoreCase(fchimeric) ? null : new TextStreamWriter(fchimeric, true, false, true, FileFormat.SAM));
TextStreamWriter unmapped=("null".equalsIgnoreCase(funmapped) ? null : new TextStreamWriter(funmapped, true, false, true, FileFormat.SAM));
if(plus!=null){plus.start();}
if(minus!=null){minus.start();}
if(chimeric!=null){chimeric.start();}
if(unmapped!=null){unmapped.start();}
for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
if(line.charAt(0)=='@'){
if(plus!=null){plus.println(line);}
if(minus!=null){minus.println(line);}
if(chimeric!=null){chimeric.println(line);}
if(unmapped!=null){unmapped.println(line);}
}else{
SamLine sl=new SamLine(line);
reads++;
// bases+=sl.seq.length();
bases+=sl.seq.length;
if(!sl.mapped() || !sl.nextMapped() || !sl.hasMate() || !sl.primary()){
if(unmapped!=null){unmapped.println(line);}
ureads++;
// System.out.println("unmapped: "+sl.mapped()+", "+sl.nextMapped()+", "+sl.hasMate()+", "+!sl.primary());
}else if(!sl.pairedOnSameChrom() || sl.strand()==sl.nextStrand()){
if(chimeric!=null){chimeric.println(line);}
creads++;
// System.out.println("chimeric: "+sl.pairedOnSameChrom()+", "+(sl.strand()==sl.nextStrand())+", "+sl.strand()+", "+sl.nextStrand()+", "+new String(sl.rname())+", "+new String(sl.rnext()));
}else if((sl.firstFragment() ? sl.strand() : sl.nextStrand())==Shared.PLUS){
if(plus!=null){plus.println(line);}
preads++;
}else if((sl.firstFragment() ? sl.strand() : sl.nextStrand())==Shared.MINUS){
if(minus!=null){minus.println(line);}
mreads++;
}else{
throw new RuntimeException("Unhandled case: "+sl.firstFragment()+", "+sl.lastFragment()+", "+sl.strand()+", "+sl.nextStrand()+"\n"+sl+"\n");
}
}
}
if(plus!=null){plus.poisonAndWait();}
if(minus!=null){minus.poisonAndWait();}
if(chimeric!=null){chimeric.poisonAndWait();}
if(unmapped!=null){unmapped.poisonAndWait();}
t.stop();
outstream.println(Tools.timeReadsBasesProcessed(t, reads, bases, 8));
outstream.println("Plus Reads: "+preads);
outstream.println("Minus Reads: "+mreads);
outstream.println("Chimeric Reads: "+creads);
outstream.println("Unmapped Reads: "+ureads);
}
private PrintStream outstream=System.err;
}
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