import java.io.*;
public class MemoConsumptionExplore1 {
    public static void main(String[] args) throws IOException {
        new MemoConsumptionExplore1().run();
    }
    void run() throws IOException {
        String file = "c:\\java_test_int_1e7.txt";
        BufferedReader fr=new BufferedReader(new FileReader(file));
        String s;
        while ( fr.ready() ) {
            s = fr.readLine();
        }
    }
}

...
        StringBuilder b;
        while ( fr.ready() ) {
            b = new StringBuilder(fr.readLine());
        }
        ...

import java.io.*;
import java.math.BigInteger;
import java.util.*;
public class FileReaderTest {
    StreamTokenizer in;
    BufferedWriter bw;
    final String FILE_NAME="c:\\bigints.txt";
    public static void main(String[] args) throws IOException {
        new FileReaderTest().run();
    }
    void run() throws IOException {
        bw = new BufferedWriter(new FileWriter(FILE_NAME));
        int N = 10; // 000;
        BigInteger b;
        Random r = new Random();
        for (int i = 0; i < N; i++) {
           b = new BigInteger(128, r);
           bw.write(b.toString());
           bw.newLine();
        }
        bw.close();        
        //---------------------------------------------------------------------
        in = new StreamTokenizer(new BufferedReader(new FileReader(FILE_NAME))); 
        
        HashSet<BigInteger> hsPrimes = new HashSet<BigInteger>();
        int i=0;
        BigInteger p;
        while (in.nextToken() != StreamTokenizer.TT_EOF) {
            // ? how to cast next token as String ?
            //p.isProbablePrime(4);
            i++;
        }
        System.out.println("total primes in list: "+i);
    }
} // end of class FileReaderTest

...
        while (in.nextToken() != StreamTokenizer.TT_EOF) {
            // ? how to cast next token as String ?
            String s = in.sval;
            System.out.println("s="+s);
            p=new BigInteger(s);
            //p.isProbablePrime(4);
            i++;
        }

run:
s= null  
Exception in thread "main" java.lang. NullPointerException
	at java.math.BigInteger.<init>(BigInteger.java:271)
	at java.math.BigInteger.<init>(BigInteger.java:451)
	at DataStructures.FileReaderTest.run(FileReaderTest.java:33)
	at DataStructures.FileReaderTest.main(FileReaderTest.java:10)
Java Result: 1

if(s == null){
  continue;
}

        int i=0;
        BigInteger p;
        while (in.nextToken() != StreamTokenizer.TT_EOF) {
            // ? how to cast next token as String ?
            String s = in.sval;
            if (s==null) {
                continue;
            }
            System.out.println("s="+s);
            p=new BigInteger(s);
            //p.isProbablePrime(4);
            i++;
        }
        System.out.println("total primes in list: "+i);

run:
total primes in list: 0
BUILD SUCCESSFUL (total time: 0 seconds)

import java.io.*;
import java.math.BigInteger;
import java.util.*;
public class FileReaderTest {
    StreamTokenizer in;
    BufferedWriter bw;
    final String FILE_NAME="c:\\bigints.txt";
    public static void main(String[] args) throws IOException {
        new FileReaderTest().run();
    }
    void run() throws IOException {
        bw = new BufferedWriter(new FileWriter(FILE_NAME));
        int N = 1000;
        BigInteger b;
        Random r = new Random();
        for (int i = 0; i < N; i++) {
           b = new BigInteger(164, r);
           bw.write(b.toString());
           bw.newLine();
        }
        bw.close();        
        //---------------------------------------------------------------------
        in = new StreamTokenizer(new BufferedReader(new FileReader(FILE_NAME))); 

        // commands to handle result of in.sval always as String 
        // during read of large integer numbers:
        in.resetSyntax();
        in.wordChars('0', '9');
        in.whitespaceChars('\r', '\r');
        in.whitespaceChars('\n', '\n');
        
        TreeSet<BigInteger> hsPrimes = new TreeSet<BigInteger>();
        int i=0;
        BigInteger p;
        while (in.nextToken() != StreamTokenizer.TT_EOF) {
            String s = in.sval;
            p=new BigInteger(s);
            if (p.isProbablePrime(4)) {
                hsPrimes.add(p);
                i++;
            }
        }
        
        for( BigInteger hsx : hsPrimes ) {
            System.out.println(hsx);
        }
        System.out.println("\nTotal primes in list: "+i);
    }
} // end of class FileReaderTest

run:
4612619974923713006482770328350670622019371639077
7189510052098150038091299601582044773577185859157
8407730875700650704020123844924590906417514732821
8867142705835293079085585841666931214505993454957
10354240823379391054805894162827628843337663603409
17142209726205277927415048885733089334431596809097
22323063444758797701968114793566179667817460514761
23159319033082054596615693780239344377534899380351

Total primes in list: 8

        br = new BufferedReader(new FileReader(FILE_NAME));
        char[] buf = new char[60]; // 60 = гарантированно больше, чем число десятичных знаков в сгенерённых BigInt-числах
        while (br.ready()) {
            // br.read(buf, off, len); // вот тут - что надо делать ?
        }

        br = new BufferedReader(new FileReader(FILE_NAME));
        char[] buf = new char[60];
        int k=0;
        List clist;
        //System.out.println(br.markSupported());
        BigDecimal d;
        while (br.ready() && k<10) {
            br.mark(60);
            br.read(buf, 0, 60);
            int crlf=0;
            for (int j = 0; j < buf.length; j++) {
                if (buf[j]=='\r') {
                    crlf=j;
                }
                if (j>=crlf-1) {
                    buf[j]=' ';
                }
            }
            br.reset();
            br.read(buf, 0, crlf);
            System.out.println((new String(buf)));
            d=new BigDecimal(buf);
            k++;
        }

100004163706653319627008032022914325716                     
Exception in thread "main" java.lang.NumberFormatException
	at java.math.BigDecimal.<init>(BigDecimal.java:459)
	at java.math.BigDecimal.<init>(BigDecimal.java:590)
	at DataStructures.ChkBigPrimes2.run(ChkBigPrimes2.java:48)
	at DataStructures.ChkBigPrimes2.main(ChkBigPrimes2.java:11)
Java Result: 1