Creating , Serializing data using apache avro and ga4gh schema ( vcf ngs variant json )

Makefile

.PHONY:all
all: avro-tools-1.7.7.jar schemas-0.5.1/src/main/resources/avro/variants.avpr src/test/TestAvro.java
	rm -rf generated
	mkdir -p generated
	#generate java classes
	java -jar $< compile protocol schemas-0.5.1/src/main/resources/avro/ ./generated
	#compile classes
	javac -d generated -cp avro-tools-1.7.7.jar -sourcepath generated:src generated/org/ga4gh/*.java src/test/TestAvro.java
	# archive
	jar cvf generated/ga4gh.jar -C generated org -C generated test
	# run
	java -cp avro-tools-1.7.7.jar:generated/ga4gh.jar test.TestAvro > variant.avro
	#decode
	 java -jar avro-tools-1.7.7.jar tojson variant.avro
	
	
avro-tools-1.7.7.jar :
	curl -L -o $@ "http://www.eng.lsu.edu/mirrors/apache/avro/avro-1.7.7/java/$@"

schemas-0.5.1/src/main/resources/avro/variants.avpr: avro-tools-1.7.7.jar  schemas-0.5.1/src/main/resources/avro/variants.avdl
	java -jar $< idl $(filter %.avdl,$^) > $@

schemas-0.5.1/src/main/resources/avro/variants.avdl :
	rm -rf schemas-0.5.1
	curl -L -o schema.zip "https://github.com/ga4gh/schemas/archive/v0.5.1.zip"
	unzip schema.zip
	rm schema.zip

output.txt

{"id":"rs1","variantSetId":"id1","names":[],"created":{"long":1434624257608},"updated":{"long":1434624257608},"referenceName":"chr1","start":1,"end":1,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs2","variantSetId":"id2","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":2,"end":2,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs3","variantSetId":"id3","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":3,"end":3,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs4","variantSetId":"id4","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":4,"end":4,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs5","variantSetId":"id5","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":5,"end":5,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs6","variantSetId":"id6","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":6,"end":6,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs7","variantSetId":"id7","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":7,"end":7,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs8","variantSetId":"id8","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":8,"end":8,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}
{"id":"rs9","variantSetId":"id9","names":[],"created":{"long":1434624257635},"updated":{"long":1434624257635},"referenceName":"chr1","start":9,"end":9,"referenceBases":"A","alternateBases":["C","T"],"info":{},"calls":[]}

TestAvro.java

package test;
import org.apache.avro.*;
import org.apache.avro.io.*;
import org.apache.avro.file.*;
import org.apache.avro.specific.*;
import org.ga4gh.*;
import java.util.*;

public class TestAvro
	{
	private void run() throws Exception
		{

		
		//Write data of a schema. 
		DatumWriter<GAVariant> variantWriter = new SpecificDatumWriter<GAVariant>( GAVariant.getClassSchema() );
		DataFileWriter<GAVariant> dataWriter = new DataFileWriter<GAVariant>(variantWriter);
		dataWriter.create(GAVariant.getClassSchema(), System.out);
		for(int i=1;i< 10;++i)
			{
			GAVariant variant =  GAVariant.newBuilder()
				.setReferenceName("chr1")
				.setStart(i)
				.setEnd(i)
				.setId("rs"+i)
				.setVariantSetId("id"+i)
				.setReferenceBases("A")
				.setCreated(System.currentTimeMillis())
				.setUpdated(System.currentTimeMillis())
				.setAlternateBases(Arrays.asList("C","T"))
				.build()
				;
			dataWriter.append(variant);
			}
		
		
		
		dataWriter.close();
		}
		
	public static void main(String args[])
		{
		try
			{
			TestAvro app = new TestAvro();
			app.run();
			}
		catch(Exception err)
			{
			err.printStackTrace();
			}
		}
	}