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package stream;
import java.io.PrintStream;
import java.util.ArrayDeque;
import fileIO.FileFormat;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import structures.ListNum;
/**
* Loads multiple sam files rapidly with multiple threads.
*
* @author Brian Bushnell
* @date March 6, 2019
*
*/
public class SamStreamerMF {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
/**
* Code entrance from the command line.
* @param args Command line arguments
*/
public static final void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
int threads=Shared.threads();
if(args.length>1){threads=Integer.parseInt(args[1]);}
SamStreamerMF x=new SamStreamerMF(args[0].split(","), threads, false, -1);
//Run the object
x.start();
x.test();
t.stop("Time: ");
}
/**
* Constructor.
*/
public SamStreamerMF(String[] fnames_, int threads_, boolean saveHeader_, long maxReads_){
this(FileFormat.testInput(fnames_, FileFormat.SAM, null, true, false), threads_, saveHeader_, maxReads_);
}
/**
* Constructor.
*/
public SamStreamerMF(FileFormat[] ffin_, int threads_, boolean saveHeader_, long maxReads_){
fname=ffin_[0].name();
threads=threads_;
ffin=ffin_;
saveHeader=saveHeader_;
}
/*--------------------------------------------------------------*/
/*---------------- Outer Methods ----------------*/
/*--------------------------------------------------------------*/
final void test(){
for(ListNum<Read> list=nextReads(); list!=null; list=nextReads()){
if(verbose){outstream.println("Got list of size "+list.size());}
}
}
/** Create read streams and process all data */
public final void start(){
//Reset counters
readsProcessed=0;
basesProcessed=0;
//Process the reads in separate threads
spawnThreads();
if(verbose){outstream.println("Finished; closing streams.");}
}
public final ListNum<Read> nextList(){return nextReads();}
public final ListNum<Read> nextReads(){
ListNum<Read> list=null;
assert(activeStreamers!=null);
synchronized(activeStreamers){
if(activeStreamers.isEmpty()){return null;}
while(list==null && !activeStreamers.isEmpty()){
SamReadStreamer srs=activeStreamers.poll();
list=srs.nextReads();
if(list!=null){activeStreamers.add(srs);}
else{
readsProcessed+=srs.readsProcessed;
basesProcessed+=srs.basesProcessed;
if(srs.header!=null){
SamReadInputStream.setSharedHeader(srs.header);
}
if(!streamerSource.isEmpty()){
srs=streamerSource.poll();
srs.start();
activeStreamers.add(srs);
}
}
}
}
return list;
}
// public abstract ListNum<SamLine> nextLines();
/*--------------------------------------------------------------*/
/*---------------- Inner Methods ----------------*/
/*--------------------------------------------------------------*/
/** Spawn process threads */
void spawnThreads(){
final int maxActive=Tools.max(2, Tools.min((Shared.threads()+4)/5, ffin.length, MAX_FILES));
streamerSource=new ArrayDeque<SamReadStreamer>(ffin.length);
activeStreamers=new ArrayDeque<SamReadStreamer>(maxActive);
for(int i=0; i<ffin.length; i++){
SamReadStreamer srs=new SamReadStreamer(ffin[i], threads, saveHeader, maxReads);
streamerSource.add(srs);
}
while(activeStreamers.size()<maxActive && !streamerSource.isEmpty()){
SamReadStreamer srs=streamerSource.poll();
srs.start();
activeStreamers.add(srs);
}
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
/** Primary input file path */
protected String fname;
/*--------------------------------------------------------------*/
/** Number of reads processed */
protected long readsProcessed=0;
/** Number of bases processed */
protected long basesProcessed=0;
/** Quit after processing this many input reads; -1 means no limit */
protected long maxReads=-1;
/*--------------------------------------------------------------*/
/*---------------- Final Fields ----------------*/
/*--------------------------------------------------------------*/
final boolean saveHeader;
/** Primary input file */
final FileFormat[] ffin;
/** Readers */
// final SamReadStreamer[] streamers;
private ArrayDeque<SamReadStreamer> streamerSource;
private ArrayDeque<SamReadStreamer> activeStreamers;
final int threads;
/*--------------------------------------------------------------*/
/*---------------- Static Fields ----------------*/
/*--------------------------------------------------------------*/
public static int DEFAULT_THREADS=6;
public static int MAX_FILES=8;
/*--------------------------------------------------------------*/
/*---------------- Common Fields ----------------*/
/*--------------------------------------------------------------*/
/** Print status messages to this output stream */
protected PrintStream outstream=System.err;
/** Print verbose messages */
public static final boolean verbose=false;
public static final boolean verbose2=false;
/** True if an error was encountered */
public boolean errorState=false;
}
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