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package stream;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.Set;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Shared;
import shared.Tools;
import structures.ListNum;
/**
* Allows output of reads to multiple different output streams.
* @author Brian Bushnell
* @date Apr 12, 2015
*
*/
public class MultiCros {
public static void main(String[] args){
String in=args[0];
String pattern=args[1];
ArrayList<String> names=new ArrayList<String>();
for(int i=2; i<args.length; i++){
names.add(args[i]);
}
final int buff=Tools.max(16, 2*Shared.threads());
MultiCros mcros=new MultiCros(pattern, null, false, false, false, false, false, FileFormat.FASTQ, buff);
ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, true, false, in);
cris.start();
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
ArrayListSet als=new ArrayListSet(false);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
for(Read r1 : reads){
als.add(r1, names);
}
cris.returnList(ln);
if(mcros!=null){mcros.add(als, ln.id);}
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
cris.returnList(ln);
if(mcros!=null){mcros.add(als, ln.id);}
ReadWrite.closeStreams(cris);
ReadWrite.closeStreams(mcros);
}
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public MultiCros(String pattern1_, String pattern2_,
boolean ordered_, boolean overwrite_, boolean append_, boolean allowSubprocess_, boolean useSharedHeader_, int defaultFormat_, int maxSize_){
assert(pattern1_!=null && pattern1_.indexOf('%')>=0);
assert(pattern2_==null || pattern1_.indexOf('%')>=0);
if(pattern2_==null && pattern1_.indexOf('#')>=0){
pattern1=pattern1_.replaceFirst("#", "1");
pattern2=pattern1_.replaceFirst("#", "2");
}else{
pattern1=pattern1_;
pattern2=pattern2_;
}
ordered=ordered_;
overwrite= overwrite_;
append=append_;
allowSubprocess=allowSubprocess_;
useSharedHeader=useSharedHeader_;
defaultFormat=defaultFormat_;
maxSize=maxSize_;
streamList=new ArrayList<ConcurrentReadOutputStream>();
streamMap=new LinkedHashMap<String, ConcurrentReadOutputStream>();
}
/*--------------------------------------------------------------*/
/*---------------- Outer Methods ----------------*/
/*--------------------------------------------------------------*/
public void add(ArrayListSet set, long listnum){
for(String s : set.getNames()){
ArrayList<Read> list=set.getAndClear(s);
if(list!=null){
add(list, listnum, s);
}
}
}
public void add(ArrayList<Read> list, long listnum, String name){
ConcurrentReadOutputStream ros=getStream(name);
ros.add(list, listnum);
}
public void close(){
for(ConcurrentReadOutputStream cros : streamList){cros.close();}
}
public void join(){
for(ConcurrentReadOutputStream cros : streamList){cros.join();}
}
public void resetNextListID(){
for(ConcurrentReadOutputStream cros : streamList){cros.resetNextListID();}
}
public String fname(){return pattern1;}
/** Return true if this stream has detected an error */
public boolean errorState(){
boolean b=errorState;
for(ConcurrentReadOutputStream cros : streamList){
b=b&&cros.errorState();
}
return b;
}
public boolean finishedSuccessfully(){
boolean b=true;
for(ConcurrentReadOutputStream cros : streamList){
b=b&&cros.finishedSuccessfully();
}
return b;
}
public Set<String> getKeys(){return streamMap.keySet();}
/*--------------------------------------------------------------*/
/*---------------- Inner Methods ----------------*/
/*--------------------------------------------------------------*/
private ConcurrentReadOutputStream makeStream(String name){
String s1=pattern1.replaceFirst("%", name);
String s2=pattern2==null ? null : pattern2.replaceFirst("%", name);
final FileFormat ff1=FileFormat.testOutput(s1, defaultFormat, null, allowSubprocess, overwrite, append, ordered);
final FileFormat ff2=FileFormat.testOutput(s2, defaultFormat, null, allowSubprocess, overwrite, append, ordered);
ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ff1, ff2, maxSize, null, useSharedHeader);
return ros;
}
/*--------------------------------------------------------------*/
/*---------------- Getters ----------------*/
/*--------------------------------------------------------------*/
public ConcurrentReadOutputStream getStream(String name){
ConcurrentReadOutputStream ros=streamMap.get(name);
if(ros==null){
synchronized(streamMap){
ros=streamMap.get(name);
if(ros==null){
ros=makeStream(name);
ros.start();
streamList.add(ros);
streamMap.put(name, ros);
}
}
}
return ros;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
public final String pattern1, pattern2;
public final ArrayList<ConcurrentReadOutputStream> streamList;
public final LinkedHashMap<String, ConcurrentReadOutputStream> streamMap;
public final boolean ordered;
boolean errorState=false;
boolean started=false;
final boolean overwrite;
final boolean append;
final boolean allowSubprocess;
final int defaultFormat;
final int maxSize;
final boolean useSharedHeader;
/*--------------------------------------------------------------*/
/*---------------- Static Fields ----------------*/
/*--------------------------------------------------------------*/
public static boolean verbose=false;
}
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