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package stream;
import java.util.ArrayList;
import fileIO.ByteFile;
import fileIO.FileFormat;
import hiseq.IlluminaHeaderParser2;
import shared.Shared;
import structures.ByteBuilder;
public class FastqReadInputStream extends ReadInputStream {
public static void main(String[] args){
FastqReadInputStream fris=new FastqReadInputStream(args[0], true);
Read r=fris.next();
System.out.println(r.toText(false));
}
public FastqReadInputStream(String fname, boolean allowSubprocess_){
this(FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess_, false));
}
public FastqReadInputStream(FileFormat ff){
if(verbose){System.err.println("FastqReadInputStream("+ff+")");}
flag=(Shared.AMINO_IN ? Read.AAMASK : 0);
stdin=ff.stdio();
shrinkHeaders=FASTQ.SHRINK_HEADERS;
if(!ff.fastq()){
System.err.println("Warning: Did not find expected fastq file extension for filename "+ff.name());
}
if(FASTQ.PARSE_CUSTOM){
try {
String s[]=ff.name().split("_");
// maxSnps=toNumber(s[3]);
// maxInss=toNumber(s[4]);
// maxDels=toNumber(s[5]);
// maxSubs=toNumber(s[6]);
// s=s[8].split("\\.");
//
// s=s[0].split("-");
// if(s.length!=8 && s.length!=9){
// if(Shared.WINDOWS){System.err.println("Note: Filename indicates non-synthetic data, but FASTQ.PARSE_CUSTOM="+FASTQ.PARSE_CUSTOM);}
// }
// minChrom=Gene.toChromosome(s[0]);
// maxChrom=Gene.toChromosome(s[1]);
} catch (Exception e) {
// TODO Auto-generated catch block
// e.printStackTrace();
// if(Shared.WINDOWS){System.err.println("Note: Filename indicates non-synthetic data, but FASTQ.PARSE_CUSTOM="+FASTQ.PARSE_CUSTOM);}
}
}
// interleaved=false;
interleaved=ff.interleaved();//(ff.stdio()) ? FASTQ.FORCE_INTERLEAVED : FASTQ.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=FASTQ.toReadList(tf, BUF_LEN, nextReadID, interleaved, flag);
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.");
}
}else if(shrinkHeaders) {//Kind of slow to regenerate strings but oh well
for(Read r : buffer) {shrinkHeader(r, r.mate);}
}
}
private void shrinkHeader(Read r1, Read r2) {
ihp.parse(r1.id);
if(!ihp.canShrink()) {return;}
bbh.clear().colon().colon().colon();
ihp.appendCoordinates(bbh).space().append(1).colon();
r1.id=bbh.toString();
if(r2!=null) {
bbh.set(bbh.length-2, (byte)'2');
r2.id=bbh.toString();
}
}
@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;}
@Override
public String fname(){return tf.name();}
/** Return true if this stream has detected an error */
@Override
public boolean errorState(){return errorState || FASTQ.errorState();}
private ArrayList<Read> buffer=null;
private int next=0;
private final ByteFile tf;
private final boolean interleaved;
private final int flag;
private boolean shrinkHeaders;
private final ByteBuilder bbh=new ByteBuilder(128);
private final IlluminaHeaderParser2 ihp=new IlluminaHeaderParser2();
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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