org.broadinstitute.hellbender.engine.spark.datasources

Class VariantsSparkSink.SparkVCFOutputFormat

java.lang.Object

org.apache.hadoop.mapreduce.OutputFormat<K,V>

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.VariantContextWritable>

org.seqdoop.hadoop_bam.VCFOutputFormat<K>

org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<org.apache.hadoop.io.NullWritable>

org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink.SparkVCFOutputFormat

Direct Known Subclasses:

VariantsSparkSink.SparkHeaderlessVCFOutputFormat

Enclosing class:

VariantsSparkSink

public static class VariantsSparkSink.SparkVCFOutputFormat
extends org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<org.apache.hadoop.io.NullWritable>

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.Counter

Field Summary

Fields

Modifier and Type	Field and Description
static htsjdk.variant.vcf.VCFHeader	vcfHeader

Fields inherited from class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat

header, WRITE_HEADER_PROPERTY

Fields inherited from class org.seqdoop.hadoop_bam.VCFOutputFormat

format, OUTPUT_VCF_FORMAT_PROPERTY

Fields inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

BASE_OUTPUT_NAME, COMPRESS, COMPRESS_CODEC, COMPRESS_TYPE, OUTDIR, PART

Constructor Summary

Constructors

Constructor and Description
SparkVCFOutputFormat()

Method Summary

Modifier and Type	Method and Description
void	checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)
org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.NullWritable,org.seqdoop.hadoop_bam.VariantContextWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
static void	setVCFHeader(htsjdk.variant.vcf.VCFHeader header)

Methods inherited from class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat

getHeader, getRecordWriter, getRecordWriter, readHeaderFrom, readHeaderFrom, setHeader

Methods inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

getCompressOutput, getDefaultWorkFile, getOutputCommitter, getOutputCompressorClass, getOutputName, getOutputPath, getPathForWorkFile, getUniqueFile, getWorkOutputPath, setCompressOutput, setOutputCompressorClass, setOutputName, setOutputPath

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

vcfHeader

public static htsjdk.variant.vcf.VCFHeader vcfHeader

Constructor Detail

SparkVCFOutputFormat

public SparkVCFOutputFormat()

Method Detail

setVCFHeader

public static void setVCFHeader(htsjdk.variant.vcf.VCFHeader header)

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.NullWritable,org.seqdoop.hadoop_bam.VariantContextWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                                                                                                                                          throws java.io.IOException

Overrides:

getRecordWriter in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<org.apache.hadoop.io.NullWritable>

Throws:

java.io.IOException

checkOutputSpecs

public void checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)
                      throws java.io.IOException

Overrides:

checkOutputSpecs in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<org.apache.hadoop.io.NullWritable,org.seqdoop.hadoop_bam.VariantContextWritable>

Throws:

java.io.IOException