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package stream;
import java.util.ArrayList;
import fileIO.ByteFile;
import fileIO.FileFormat;
import shared.KillSwitch;
import shared.Shared;
import shared.Tools;
public class OnelineReadInputStream extends ReadInputStream {
public static void main(String[] args){
OnelineReadInputStream fris=new OnelineReadInputStream(args[0], true);
Read r=fris.next();
System.out.println(r.toText(false));
}
public OnelineReadInputStream(String fname, boolean allowSubprocess_){
this(FileFormat.testInput(fname, FileFormat.ONELINE, null, allowSubprocess_, false));
}
public OnelineReadInputStream(FileFormat ff){
if(verbose){System.err.println("FastqReadInputStream("+ff+")");}
stdin=ff.stdio();
if(!ff.oneline()){
System.err.println("Warning: Did not find expected oneline file extension for filename "+ff.name());
}
// interleaved=false;
// assert(false) : "TODO: Detect interleaved.";
interleaved=FASTQ.FORCE_INTERLEAVED; //(ff.stdio()) ? FASTQ_X.FORCE_INTERLEAVED : FASTQ_X.isInterleaved(ff.name(), false);
tf=ByteFile.makeByteFile(ff);
// assert(false) : interleaved;
}
@Override
public void start() {
// if(cris!=null){cris.start();}
}
@Override
public boolean hasMore() {
if(buffer==null || next>=buffer.size()){
if(tf.isOpen()){
fillBuffer();
}else{
assert(generated>0) : "Was the file empty?";
}
}
return (buffer!=null && next<buffer.size());
}
@Override
public Read next() {
if(!hasMore()){return null;}
Read r=buffer.set(next, null);
next++;
consumed++;
return r;
}
@Override
public synchronized ArrayList<Read> nextList() {
if(next!=0){throw new RuntimeException("'next' should not be used when doing blockwise access.");}
if(buffer==null || next>=buffer.size()){fillBuffer();}
ArrayList<Read> list=buffer;
buffer=null;
if(list!=null && list.size()==0){list=null;}
consumed+=(list==null ? 0 : list.size());
return list;
}
private synchronized void fillBuffer(){
assert(buffer==null || next>=buffer.size());
buffer=null;
next=0;
buffer=toReadList();
int bsize=(buffer==null ? 0 : buffer.size());
// nextReadID+=bsize;
if(bsize<BUF_LEN){tf.close();}
generated+=bsize;
if(buffer==null){
if(!errorState){
errorState=true;
System.err.println("Null buffer in FastqReadInputStream.");
}
}
}
private ArrayList<Read> toReadList(){
ArrayList<Read> list=new ArrayList<Read>(BUF_LEN);
Read r1=null, r2=null;
long sum=0;
for(byte[] line=tf.nextLine(); line!=null; line=tf.nextLine()){
int index=Tools.lastIndexOf(line, (byte)'\t');
String id=new String(line, 0, index);
byte[] bases=KillSwitch.copyOfRange(line, index+1, line.length);
sum+=bases.length;
Read r=new Read(bases, null, id, nextReadID);
if(r1==null){
r1=r;
}else{
r2=r;
r1.mate=r2;
r2.mate=r1;
}
if(interleaved==(r2!=null)){
list.add(r1);
r1=r2=null;
nextReadID++;
if(list.size()>=BUF_LEN || sum>=MAX_DATA){break;}
}
}
return list;
}
@Override
public boolean close(){
if(verbose){System.err.println("Closing "+this.getClass().getName()+" for "+tf.name()+"; errorState="+errorState);}
errorState|=tf.close();
if(verbose){System.err.println("Closed "+this.getClass().getName()+" for "+tf.name()+"; errorState="+errorState);}
return errorState;
}
@Override
public synchronized void restart() {
generated=0;
consumed=0;
next=0;
nextReadID=0;
buffer=null;
tf.reset();
}
@Override
public boolean paired() {return interleaved;}
/** Return true if this stream has detected an error */
@Override
public boolean errorState(){return errorState;}
@Override
public String fname(){return tf.name();}
private ArrayList<Read> buffer=null;
private int next=0;
private final ByteFile tf;
private final boolean interleaved;
private final int BUF_LEN=Shared.bufferLen();;
private final long MAX_DATA=Shared.bufferData(); //TODO - lot of work for unlikely case of super-long fastq reads. Must be disabled for paired-ends.
public long generated=0;
public long consumed=0;
private long nextReadID=0;
public final boolean stdin;
public static boolean verbose=false;
}
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