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package stream;
import java.util.ArrayList;
import align2.RandomReads3;
import dna.Data;
import shared.Shared;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Sep 10, 2014
*
*/
public class RandomReadInputStream3 extends ReadInputStream {
public RandomReadInputStream3(long number_, boolean paired_){
Data.setGenome(Data.GENOME_BUILD);
number=number_;
paired=paired_;
maxChrom=Data.numChroms;
minQual=6;
midQual=18;
maxQual=30;
restart();
}
public RandomReadInputStream3(long number_, int minreadlen_, int maxreadlen_,
int maxSnps_, int maxInss_, int maxDels_, int maxSubs_,
float snpRate_, float insRate_, float delRate_, float subRate_,
int maxInsertionLen_, int maxDeletionLen_, int maxSubLen_,
int minChrom_, int maxChrom_, boolean paired_,
int minQual_, int midQual_, int maxQual_){
Data.setGenome(Data.GENOME_BUILD);
number=number_;
minreadlen=minreadlen_;
maxreadlen=maxreadlen_;
maxInsertionLen=maxInsertionLen_;
maxSubLen=maxSubLen_;
maxDeletionLen=maxDeletionLen_;
minInsertionLen=1;
minSubLen=1;
minDeletionLen=1;
minNLen=1;
minChrom=minChrom_;
maxChrom=maxChrom_;
maxSnps=maxSnps_;
maxInss=maxInss_;
maxDels=maxDels_;
maxSubs=maxSubs_;
snpRate=snpRate_;
insRate=insRate_;
delRate=delRate_;
subRate=subRate_;
paired=paired_;
minQual=(byte) minQual_;
midQual=(byte) midQual_;
maxQual=(byte) maxQual_;
restart();
}
@Override
public void start() {}
@Override
public boolean hasMore() {
return number>consumed;
}
@Override
public Read next() {
if(consumed>=number){return null;}
if(buffer==null || next>=buffer.size()){fillBuffer();}
Read r=buffer.get(next);
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(consumed>=number){return null;}
if(buffer==null || next>=buffer.size()){fillBuffer();}
ArrayList<Read> r=buffer;
buffer=null;
if(r!=null && r.size()==0){r=null;}
consumed+=(r==null ? 0 : r.size());
// assert(false) : r.size();
return r;
}
private synchronized void fillBuffer(){
buffer=null;
next=0;
long toMake=number-generated;
if(toMake<1){return;}
toMake=Tools.min(toMake, BUF_LEN);
ArrayList<Read> reads=rr.makeRandomReadsX((int)toMake, minreadlen, maxreadlen, -1,
maxSnps, maxInss, maxDels, maxSubs, maxNs,
snpRate, insRate, delRate, subRate, NRate,
minInsertionLen, minDeletionLen, minSubLen, minNLen,
maxInsertionLen, maxDeletionLen, maxSubLen, maxNLen,
minChrom, maxChrom,
minQual, midQual, maxQual);
generated+=reads.size();
assert(generated<=number);
buffer=reads;
// assert(false) : reads.size()+", "+toMake;
}
@Override
public synchronized void restart(){
next=0;
buffer=null;
consumed=0;
generated=0;
rr=new RandomReads3(1, paired);
}
@Override
public boolean close() {return false;}
@Override
public boolean paired() {
return paired;
}
@Override
public String fname(){return "random";}
private ArrayList<Read> buffer=null;
private int next=0;
private final int BUF_LEN=Shared.bufferLen();;
public long generated=0;
public long consumed=0;
public long number=100000;
public int minreadlen=100;
public int maxreadlen=100;
public int maxInsertionLen=6;
public int maxSubLen=6;
public int maxDeletionLen=100;
public int maxNLen=6;
public int minInsertionLen=1;
public int minSubLen=1;
public int minDeletionLen=1;
public int minNLen=1;
public int minChrom=1;
public int maxChrom=22;
public int maxSnps=4;
public int maxInss=2;
public int maxDels=2;
public int maxSubs=2;
public int maxNs=2;
public float snpRate=0.5f;
public float insRate=0.25f;
public float delRate=0.25f;
public float subRate=0.10f;
public float NRate=0.10f;
public final boolean paired;
public final byte minQual;
public final byte midQual;
public final byte maxQual;
private RandomReads3 rr;
}
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