Have to add extra line "String x=in.readLine();" after reading character "sec=(char)in.read();" otherwise program is not proceeding further to take more inputs, see comment below in code. Please note I don't want to use scanner class.
import java.io.*;
class marks
{
public static void main(String args[])
{
    BufferedReader in=new BufferedReader(new InputStreamReader(System.in));
    int rl,m1,m2,m3,tot=0;
    String nm,cl;
    nm=cl="";
    char sec='A';
    double avg=0.0d;
    try
    {
        System.out.println("Enter the information of the student");
        System.out.print("roll no:");
        rl=Integer.parseInt(in.readLine());
    System.out.print("class:");
    cl=in.readLine();
    System.out.print("section:");
    sec=(char)in.read();
    String x=in.readLine();  /* have to add this line only then marks of 3 subject can be inputed */
    System.out.println("marks of three subjects "+x);
    m1=Integer.parseInt(in.readLine());
    m2=Integer.parseInt(in.readLine());
    m3=Integer.parseInt(in.readLine());
    tot=m1+m2+m3;
    avg=tot/3.0d;
    System.out.println("total marks of the students = "+tot);
    System.out.println("avg marks of the students = "+avg);
    }
    catch (Exception e)
    {};
}
} 
 
     
     
    