Hello All,
I have the following code,
package com.java.tutorial.examples;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
public class Swapping {
/**
* @param args
*/
public static void main(String[] args) throws FileNotFoundException, IOException {
BufferedReader file1 = new BufferedReader(new FileReader("/path/1.txt"));
BufferedReader file2 = new BufferedReader(new FileReader("/path/2.txt"));
BufferedWriter writer = new BufferedWriter(new FileWriter("/path/file1_file2_distance.txt"));
BufferedWriter writer2 = new BufferedWriter(new FileWriter("/path/file1_file2_d.txt"));
int arg1 = Integer.parseInt(args[0]);
String s1 = null;
String[] s2 = new String[1000];
String s3 = null;
String[] s4 = new String[1000];
String s5=null;
String[] s6 = new String[1000];
int length1 = 0;
int length2 =0;
int length3 =0;
int length4 =0;
while((s1=file1.readLine())!=null)
{
s2=s1.split("\t");
length1 = s2.length;
while((s3=file2.readLine())!=null)
{
s4=s3.split("\t");
length2 = s4.length;
length3 = Integer.parseInt(s4[1])-Integer.parseInt(s2[1]);
if(s2[0]!=null && s4[0]!=null && s2[0].equalsIgnoreCase(s4[0]))
{
for(int i=0; i< length1;i++)
{
writer.write(s2 + "\t" );
}
for(int j=1; j< length2;j++)
{
writer.write(s4[j] + "\t" );
}
writer.write(Integer.parseInt(s4[1])-Integer.parseInt(s2[1]) + "\t" );
writer.newLine();
}
}
file2 = new BufferedReader(new FileReader("/path/2.bed"));
}
writer.close();
BufferedReader file3 = new BufferedReader(new FileReader("/path/file1_file2_distance.txt"));
while((s5=file3.readLine())!=null)
{
s6 = s5.split("\t");
length4 = s6.length;
if(Integer.parseInt(s6[length4-1])>=-arg1 && Integer.parseInt(s6[length4-1])<=arg1)
{
for(int k=0;k<length4;k++)
{
writer2.write(s6[k]+ "\t");
}
writer2.newLine();
}
}
writer2.close();
}
}
I would like to pass an argument to filter the difference generated between two columns.
I am using
javac -D 5000 prog.java
It is giving an error directory doesnot exist: -D
Can someone tell me how to pass that argument?
Thanks in advance.