C++ process in Java outputting null continuously to Bufferedreader.readline() in reader thread

Question

We are trying to create a java application that uses a C++ executable that performes an algorimth seperately. To have java and C++ communication we use cout and getline in C++ and while true loop with reader.readline in java. The problem arise when using cygwin as compiler for C++. As soon as java starts it receives null from c++ continuously. We are at a loss of what it problem is as the while loop had worked previously.

Java part

import java.io.*;


public class Main {
    private static ProcessBuilder pb;
    private static Process process;
    private static BufferedReader reader;
    private static BufferedWriter writer;

    public static void main(String[] args) throws IOException{//TransformException
        pb = new ProcessBuilder();
        pb.command("C:/Users/*USERNAME*/CLionProjects/untitled/cmake-build-debug/untitled.exe");  // C++ executable
        process = pb.start();
        reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
        writer = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
        BufferedReader inputReader = new BufferedReader(new InputStreamReader(System.in));

        ReaderThread rd = new ReaderThread(reader);
        rd.start();

        while(true){
            String input = inputReader.readLine();
            String lineToSend;
            switch(input.toLowerCase()){
                case "run":
                    String arg1 = "first";
                    String arg2 = "second";
                    lineToSend = "runExample"+" " + arg1 + " "+  arg2 + "\n";
                    writer.write(lineToSend);
                    writer.flush();
                    break;
            }
        }
    }
}

import java.io.IOException;

class ReaderThread extends Thread {
    BufferedReader reader;

    public ReaderThread(BufferedReader reader) {
        this.reader = reader;
    }

    public void run() {
        try {
            String reply;
            System.out.println("Reader thread ready");
            while (true) {
                reply = reader.readLine();
                String[] replyAsArr = {"No reply"};
                if (reply != null) {
                    replyAsArr = reply.split(" ");
                } else System.out.println("Got reply: " + reply);
                switch (replyAsArr[0]) {
                    case "result":
                        System.out.println("Got result");
                        break;
                    case "info":
                        System.out.println(reply);
                        break;
                    default:
                        System.out.println("Malformed input from cpp: " + reply);
                }

            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

C++ part (CppPart.exe)

#include <iostream>
#include <sstream>
#include <string>
#include <vector>
#include <iterator>
#include <map>

using namespace std;

void runAlgorithm() {
    cout << "result" << endl;
    cout << flush;
}

void communicateWithJava() {
    enum commands{
        ERROR,
        runExample,
    };
    map<string, commands> mapStringToEnum =
            {
                    {"error", ERROR},
                    {"runExample", runExample},
            };
    string line;
    while(getline(cin, line)) {
        istringstream buf(line);
        istream_iterator<string> beg(buf), end;
        vector<string> lineAsTokens(beg, end);
        commands switchType = mapStringToEnum[lineAsTokens[0]];
        switch (switchType) {
            case ERROR: {
                cout << "Could not understand input: "<< line << endl;
                cout << flush;
                break;
            }
            case runExample: {
                runAlgorithm();
                cout << "info " << lineAsTokens[1] << lineAsTokens[2] << endl;
                cout << flush;
                break;
            }
        }
    }
}

int main() {
    communicateWithJava();
    return 0;
}