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package jgi;
import java.io.PrintStream;
import fileIO.ByteFile;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parse;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.SamLine;
/**
* @author Brian Bushnell
* @date Jun 15, 2017
*
*/
public class SplitSam6Way {
public static void main(String[] args){
SplitSam6Way x=new SplitSam6Way(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.SplitSam6Way <input> <r1plus> <r1minus> <r1unmapped> <r2plus> <r2minus> <r2unmapped>");
outstream.println("If you do not want one of the output files, use the word 'null'.\n");
}
public SplitSam6Way(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<7){
printOptions();
System.exit(1);
}
ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
Timer t=new Timer();
long reads=0, bases=0;
long r1preads=0, r1mreads=0, r1ureads=0;
long r2preads=0, r2mreads=0, r2ureads=0;
String fin=args[0];
String fr1plus=args[1];
String fr1minus=args[2];
String fr1unmapped=args[3];
String fr2plus=args[4];
String fr2minus=args[5];
String fr2unmapped=args[6];
long maxReads=Long.MAX_VALUE;
if(args.length>7){
maxReads=Parse.parseKMG(args[7]);
}
// ByteFile.FORCE_MODE_BF1=true;
ByteFile tf=ByteFile.makeByteFile(fin, true);
ByteStreamWriter r1plus=("null".equalsIgnoreCase(fr1plus) ? null : new ByteStreamWriter(fr1plus, true, false, true, FileFormat.SAM));
ByteStreamWriter r1minus=("null".equalsIgnoreCase(fr1minus) ? null : new ByteStreamWriter(fr1minus, true, false, true, FileFormat.SAM));
ByteStreamWriter r1unmapped=("null".equalsIgnoreCase(fr1unmapped) ? null : new ByteStreamWriter(fr1unmapped, true, false, true, FileFormat.SAM));
ByteStreamWriter r2plus=("null".equalsIgnoreCase(fr2plus) ? null : new ByteStreamWriter(fr2plus, true, false, true, FileFormat.SAM));
ByteStreamWriter r2minus=("null".equalsIgnoreCase(fr2minus) ? null : new ByteStreamWriter(fr2minus, true, false, true, FileFormat.SAM));
ByteStreamWriter r2unmapped=("null".equalsIgnoreCase(fr2unmapped) ? null : new ByteStreamWriter(fr2unmapped, true, false, true, FileFormat.SAM));
if(r1plus!=null){r1plus.start();}
if(r1minus!=null){r1minus.start();}
if(r1unmapped!=null){r1unmapped.start();}
if(r2plus!=null){r2plus.start();}
if(r2minus!=null){r2minus.start();}
if(r2unmapped!=null){r2unmapped.start();}
for(byte[] line=tf.nextLine(); line!=null; line=tf.nextLine()){
if(line[0]=='@'){
if(r1plus!=null){r1plus.println(line);}
if(r1minus!=null){r1minus.println(line);}
if(r1unmapped!=null){r1unmapped.println(line);}
if(r2plus!=null){r2plus.println(line);}
if(r2minus!=null){r2minus.println(line);}
if(r2minus!=null){r2minus.println(line);}
}else{
if(reads>=maxReads){break;}
SamLine sl=new SamLine(line);
reads++;
bases+=sl.seq.length;
if(sl.pairnum()==0){
if(sl.mapped()){
if(sl.strand()==Shared.PLUS){
if(r1plus!=null){r1plus.println(line);}
r1preads++;
}else{
if(r1minus!=null){r1minus.println(line);}
r1mreads++;
}
}else{
if(r1unmapped!=null){r1unmapped.println(line);}
r1ureads++;
}
}else{
if(sl.mapped()){
if(sl.strand()==Shared.PLUS){
if(r2plus!=null){r2plus.println(line);}
r2preads++;
}else{
if(r2minus!=null){r2minus.println(line);}
r2mreads++;
}
}else{
if(r2unmapped!=null){r2unmapped.println(line);}
r2ureads++;
}
}
}
}
tf.close();
if(r1plus!=null){r1plus.poisonAndWait();}
if(r1minus!=null){r1minus.poisonAndWait();}
if(r1unmapped!=null){r1unmapped.poisonAndWait();}
if(r2plus!=null){r2plus.poisonAndWait();}
if(r2minus!=null){r2minus.poisonAndWait();}
if(r2unmapped!=null){r2unmapped.poisonAndWait();}
t.stop();
outstream.println(Tools.timeReadsBasesProcessed(t, reads, bases, 8));
outstream.println("R1 Plus Reads: "+r1preads);
outstream.println("R1 Minus Reads: "+r1mreads);
outstream.println("R1 Unmapped Reads: "+r1ureads);
outstream.println("R1 Plus Reads: "+r2preads);
outstream.println("R1 Minus Reads: "+r2mreads);
outstream.println("R1 Unmapped Reads: "+r2ureads);
}
private PrintStream outstream=System.err;
}
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