FastqReader.java

package com.ck.fastq.util;

/**
 * Created by s4553711 on 2018/5/31.
 */
public class FastqReader {
    private StdinIterator reader;
    private int head = 0;
    private int mark = 0;
    private int tail = 0;
    private byte[] buf = new byte[35 * 1024 * 1024];

    public FastqReader(StdinIterator input) {
        reader = input;
    }

    public boolean hasNext() {
        boolean fetching = true;
        while(fetching) {
            fill();
        }
    }

    public byte[] Next() {

    }

    private void fill() {
        if (!reader.hasNext()) return;
        byte[] tmp = reader.Next();
        if (head == 0 && tail == 0) {
            System.arraycopy(tmp, 0, buf, 0, tmp.length);
            mark = head = 0;
            tail = tmp.length - 1;
        } else if (tail - mark < 500) {
            byte[] tmp_buf = new byte[35 * 1024 * 1024];
            System.arraycopy(buf, head, tmp_buf, 0, tail - head + 1);
            System.arraycopy(tmp, 0, tmp_buf, tail - head + 1, tmp.length);
            tail = (tail - head + tmp.length);
            mark = mark - head;
            head = 0;
            buf = tmp_buf;
        }
    }
}

IteratorTest.java

package com.ck.fastq;

import com.ck.fastq.util.StdinIterator;

/**
 * Created by s4553711 on 2018/5/31.
 */
public class IteratorTest {
    public static void main(String[] args) {
        StdinIterator inp = new StdinIterator();
        long st = System.currentTimeMillis();
        long st_s = st;
        long accum = 0l;
        long accum_tot = accum;
        long counter = 0l;
        while(inp.hasNext()) {
            byte[] data = inp.Next();
//            System.err.format("log > Receive length: %10d / %d\n",data.length,counter);
//            for(byte b : data) {
//                System.out.print((char)b);
//            }
            counter++;
            accum += data.length;
            accum_tot += data.length;
            if (counter % 500 == 0) {
                System.err.format("Log > count: %d, rate: %6.1f MB/s\n",counter,
                        (accum/(1024*1024))/((System.currentTimeMillis() - st)/1000.0));
                st = System.currentTimeMillis();
                accum = 0l;
            }
        }
        System.err.format("Log > Avg rate %6.1f MS/s, %8.2f MB, %8.0f s\n",(accum_tot/(1024*1024))/((System.currentTimeMillis() - st_s)/1000.0),
                accum_tot/(1024.0*1024.0), (System.currentTimeMillis() - st_s)/1000.0);
    }
}

StdinIterator.java

package com.ck.fastq.util;

import java.io.BufferedInputStream;
import java.io.IOException;
import java.util.Arrays;

public class StdinIterator {
    private BufferedInputStream bis;
    private byte[] buf = new byte[10 * 1024 * 1024];
    private int nRead;

    public StdinIterator() {
        bis = new BufferedInputStream(new BufferedInputStream(System.in, 8 * 1024));
    }

    public boolean hasNext() {
        try {
            nRead = bis.read(buf, 0, buf.length);
        } catch (IOException e) {
            e.printStackTrace();
        }
        return nRead != -1;
    }

    public byte[] Next() {
        return Arrays.copyOfRange(buf, 0, nRead);
    }
}