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package stream;
import java.util.ArrayList;
import dna.Data;
import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.FileFormat;
import shared.Shared;
/**
* @author Brian Bushnell
* @date June 1, 2016
*
*/
public class HeaderInputStream extends ReadInputStream {
public static void main(String[] args){
HeaderInputStream his=new HeaderInputStream(args[0], true);
Read r=his.next();
System.out.println(r.toText(false));
his.close();
}
public HeaderInputStream(String fname, boolean allowSubprocess_){
this(FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess_, false));
}
public HeaderInputStream(FileFormat ff){
if(verbose){System.err.println("FastqReadInputStream("+ff+")");}
stdin=ff.stdio();
tf=new ByteFile1(ff);
}
@Override
public void 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(tf, BUF_LEN, nextReadID);
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.");
}
}
}
@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();
}
public static ArrayList<Read> toReadList(ByteFile tf, int maxReadsToReturn, long numericID){
byte[] line=null;
ArrayList<Read> list=new ArrayList<Read>(Data.min(8192, maxReadsToReturn));
int added=0;
// Read prev=null;
for(line=tf.nextLine(); line!=null && added<maxReadsToReturn; line=tf.nextLine()){
Read r=new Read(null, null, new String(line), numericID);
// if(interleaved){
// if(prev==null){prev=r;}
// else{
// prev.mate=r;
// r.mate=prev;
// r.setPairnum(1);
// list.add(prev);
// added++;
// numericID++;
// prev=null;
// }
// }else
{
list.add(r);
added++;
numericID++;
}
if(added>=maxReadsToReturn){break;}
}
assert(list.size()<=maxReadsToReturn);
return list;
}
@Override
public String fname(){return tf.name();}
@Override
public boolean paired() {return false;}
/** Return true if this stream has detected an error */
@Override
public boolean errorState(){return errorState;}
private ArrayList<Read> buffer=null;
private int next=0;
private final ByteFile tf;
// private final boolean interleaved;
private final int BUF_LEN=Shared.bufferLen();;
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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