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package assemble;
import java.util.ArrayList;
import shared.KillSwitch;
import stream.ConcurrentReadInputStream;
import structures.ByteBuilder;
import structures.LongList;
/**
* @author Brian Bushnell
* @date Jul 18, 2015
*
*/
abstract class AbstractBuildThread extends Thread {
public AbstractBuildThread(int id_, int mode_, ConcurrentReadInputStream[] crisa_){
id=id_;
crisa=crisa_;
mode=mode_;
}
/** Input read stream */
final ConcurrentReadInputStream[] crisa;
final int mode;
int minCountSeedCurrent;
final int[] leftCounts=KillSwitch.allocInt1D(4);
final int[] rightCounts=KillSwitch.allocInt1D(4);
final ByteBuilder builderT=new ByteBuilder();
// final Contig tempContig=new Contig(null);
final LongList insertSizes=new LongList();
ArrayList<Contig> contigs=new ArrayList<Contig>();
long readsInT=0;
long basesInT=0;
long lowqReadsT=0;
long lowqBasesT=0;
final int id;
}
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