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package assemble;
import stream.Read;
import structures.IntList;
public class Rollback {
public Rollback(Read r){
this(r, null);
}
public Rollback(Read r, IntList counts){
id0=r.id;
flags0=r.flags;
bases0=r.bases.clone();
quals0=(r.quality==null ? null : r.quality.clone());
counts0=(counts==null ? null : counts.copy());
}
public void rollback(Read r){
rollback(r, null);
}
public void rollback(Read r, IntList counts){
r.id=id0;
r.flags=flags0;
if(r.length()==bases0.length){
System.arraycopy(bases0, 0, r.bases, 0, bases0.length);
if(quals0!=null){System.arraycopy(quals0, 0, r.quality, 0, quals0.length);}
if(counts!=null){System.arraycopy(counts0.array, 0, counts.array, 0, counts0.size);}
}else{
r.bases=bases0;
r.quality=quals0;
if(counts!=null){
counts.clear();
counts.addAll(counts0);
}
}
}
final String id0;
final int flags0;
final byte[] bases0, quals0;
public final IntList counts0;
}
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