Sample.java

package sample;

import org.jcvi.jillion.core.datastore.DataStoreException;
import org.jcvi.jillion.core.datastore.DataStoreProviderHint;
import org.jcvi.jillion.core.util.iter.StreamingIterator;
import org.jcvi.jillion.trace.fastq.FastqDataStore;
import org.jcvi.jillion.trace.fastq.FastqFileDataStoreBuilder;
import org.jcvi.jillion.trace.fastq.FastqRecord;

import java.io.File;
import java.io.IOException;
import java.util.stream.IntStream;

/**
 * Created by hd on 4/3/16.
 */
public class Sample {
    private String name;
    private static long numberOfReads = 0L;
    private static long numberOfBases = 0L;
    private static long numberOfHighQualityBases = 0L;

    public Sample() {
    }

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    public long getNumberOfReads() {
        return numberOfReads;
    }

    public void setNumberOfReads(long numberOfReads) {
        this.numberOfReads = numberOfReads;
    }

    public long getNumberOfBases() {
        return numberOfBases;
    }

    public void setNumberOfBases(long numberOfBases) {
        this.numberOfBases = numberOfBases;
    }

    public long getNumberOfHighQualityBases() {
        return numberOfHighQualityBases;
    }

    public void setNumberOfHighQualityBases(long numberOfHighQualityBases) {
        this.numberOfHighQualityBases = numberOfHighQualityBases;
    }

    @Override
    public String toString() {
        return "Sample{" +
                "name='" + name + '\'' +
                ", numberOfReads=" + numberOfReads +
                ", numberOfBases=" + numberOfBases +
                ", numberOfHighQualityBases=" + numberOfHighQualityBases +
                '}';
    }

    private void count(FastqRecord read, int high_quality) {
        incrementReadNumber(1);
        final byte[] quality = read.getQualitySequence().toArray();
        incrementNumberOfBases(quality.length);
        IntStream is = IntStream.range(0, quality.length).map(i -> quality[i]);
        is = is.parallel().filter(b -> b >= high_quality);
        incrementNumberOfHighQualityBases(is.toArray().length);
    }

    private synchronized void incrementReadNumber(int x) {
        numberOfReads += x;
    }

    private synchronized void incrementNumberOfBases(int x) {
        numberOfBases += x;
    }
    private synchronized void incrementNumberOfHighQualityBases(int x) {
        numberOfHighQualityBases += x;
    }
    
    public void calcStat(File fqFile, int highQualityThr) {
        try {
            FastqDataStore datastore = new FastqFileDataStoreBuilder(fqFile)
                    .hint(DataStoreProviderHint.ITERATION_ONLY)
                    .build();
            StreamingIterator<FastqRecord> iter = datastore.iterator();
            iter.toStream().parallel().forEach(read -> count(read, highQualityThr));
        } catch (IOException e) {
            e.printStackTrace();
        } catch (DataStoreException e) {
            e.printStackTrace();
        }
    }
}