package org.cpic;

import org.pharmgkb.parser.vcf.VcfParser;

import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.math.BigDecimal;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;

/*
 * This Java source file was auto generated by running 'gradle buildInit --type java-library'
 * by 'Mark' at '4/11/16 12:56 PM' with Gradle 2.12
 *
 * @author Mark, @date 4/11/16 12:56 PM
 */
public class Hello {
    public static void main(String[] args) {

        Path p = Paths.get(args[0]);

        try (BufferedReader reader = Files.newBufferedReader(p)) {
            new VcfParser.Builder()
                    .fromReader(reader)
                    .parseWith((metadata, position, sampleData) -> {

                        System.out.println(position.getChromosome());
                        System.out.println(position.getPosition());
                        System.out.println(position.getIds());
                        System.out.println(position.getRef());
                        System.out.println(position.getAltBases());
                        System.out.println(position.getQuality());
                    })
                    .build().parse();
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}

@@ -90,71 +90,8 @@
 er;%0A
-import java.io.InputStreamReader;%0Aimport java.math.BigDecimal;%0A
 impo
@@ -172,33 +172,8 @@
 ths;
-%0Aimport java.util.Arrays;
 %0A%0A/*
@@ -387,18 +387,16 @@
 Hello %7B%0A
-  
   public
@@ -427,28 +427,24 @@
 %5B%5D args) %7B%0A%0A
-    
     Path p =
@@ -465,20 +465,16 @@
 s%5B0%5D);%0A%0A
-    
     try 
@@ -534,22 +534,16 @@
 %7B%0A      
- 
-     
 new VcfP
@@ -566,28 +566,16 @@
         
-     
-       
 .fromRea
@@ -586,28 +586,16 @@
 reader)%0A
-            
         
@@ -644,30 +644,16 @@
 ) -%3E %7B%0A%0A
-              
         
@@ -706,38 +706,24 @@
 ;%0A          
-        
-      
 System.out.p
@@ -750,38 +750,24 @@
 osition());%0A
-              
           Sy
@@ -799,38 +799,24 @@
 .getIds());%0A
-              
           Sy
@@ -858,38 +858,24 @@
 ;%0A          
-       
-       
 System.out.p
@@ -902,38 +902,24 @@
 ltBases());%0A
-              
           Sy
@@ -971,35 +971,11 @@
     
-            %7D)%0A            
+%7D)%0A
     
@@ -992,28 +992,24 @@
 ().parse();%0A
-    
     %7D catch 
@@ -1031,22 +1031,16 @@
 %7B%0A      
-  
-    
 ex.print
@@ -1061,16 +1061,10 @@
     
-    %7D%0A  
+%7D%0A
   %7D%0A

Fix spacing.