@Before
public void setup() throws IOException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
test_vcf_output = File.createTempFile("test_vcf_output", "");
test_vcf_output.delete();
writable = new VariantContextWritable();
Configuration conf = new Configuration();
conf.set("hadoopbam.vcf.output-format", "VCF");
KeyIgnoringVCFOutputFormat<Long> outputFormat = new KeyIgnoringVCFOutputFormat<Long>(conf);
outputFormat.setHeader(readHeader());
taskAttemptContext = new TaskAttemptContextImpl(conf, mock(TaskAttemptID.class));
writer = outputFormat.getRecordWriter(taskAttemptContext, new Path("file://" + test_vcf_output));
}