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package jgi;
import java.io.PrintStream;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.Read;
import structures.ListNum;
/**
* TODO
* @author Brian Bushnell
* @date Jan 14, 2014
*
*/
public class CountUniqueness {
public void process(){
Timer t=new Timer();
for(String s : in){
process(s);
}
t.stop();
double rpnano=readsProcessed/(double)(t.elapsed);
double bpnano=basesProcessed/(double)(t.elapsed);
String rpstring=(readsProcessed<100000 ? ""+readsProcessed : readsProcessed<100000000 ? (readsProcessed/1000)+"k" : (readsProcessed/1000000)+"m");
String bpstring=(basesProcessed<100000 ? ""+basesProcessed : basesProcessed<100000000 ? (basesProcessed/1000)+"k" : (basesProcessed/1000000)+"m");
while(rpstring.length()<8){rpstring=" "+rpstring;}
while(bpstring.length()<8){bpstring=" "+bpstring;}
outstream.println("Time: \t"+t);
outstream.println("Reads Processed: "+rpstring+" \t"+Tools.format("%.2fk reads/sec", rpnano*1000000));
outstream.println("Bases Processed: "+bpstring+" \t"+Tools.format("%.2fm bases/sec", bpnano*1000));
if(errorState){
throw new RuntimeException(this.getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
private void process(Read r1, Read r2){
if(r1==null || r2==null){return;}
readsProcessed++;
basesProcessed+=r1.length();
readsProcessed++;
basesProcessed+=r2.length();
assert(false) : "TODO";
}
public void process(String fname){
final ConcurrentReadInputStream cris;
{
FileFormat ff=FileFormat.testInput(fname, FileFormat.SAM, null, true, false);
cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff, null);
if(verbose){System.err.println("Starting cris");}
cris.start(); //4567
}
{
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
for(int idx=0; idx<reads.size(); idx++){
Read r1=reads.get(idx);
Read r2=r1.mate;
assert(false);
process(r1, r2);
}
cris.returnList(ln);
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
errorState|=ReadWrite.closeStreams(cris);
}
private static final int MAX=41;
private static final int MAX2=MAX+1;
private long[][][] goodMatrix=new long[MAX2][MAX2][MAX2];
private long[][][] badMatrix=new long[MAX2][MAX2][MAX2];
private PrintStream outstream=System.err;
private boolean verbose=false;
private long maxReads=-1;
private String in[];
private String out;
private boolean overwrite=true;
private boolean append=false;
private long readsProcessed=0;
private long basesProcessed=0;
private boolean errorState=false;
}
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