org.seqdoop.hadoop_bam

Class VCFOutputFormat<K>

java.lang.Object

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

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

org.seqdoop.hadoop_bam.VCFOutputFormat<K>

Direct Known Subclasses:

KeyIgnoringVCFOutputFormat

public abstract class VCFOutputFormat<K>
extends org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,VariantContextWritable>

An abstract OutputFormat for VCF and BCF files. Only locks down the value type and stores the output format requested.

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
protected VCFFormat	format
static String	OUTPUT_VCF_FORMAT_PROPERTY A string property defining the output format to use.

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

BASE_OUTPUT_NAME, COMPRESS, COMPRESS_CODEC, COMPRESS_TYPE, OUTDIR, PART

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	VCFOutputFormat(org.apache.hadoop.conf.Configuration conf) Creates a new output format, reading OUTPUT_VCF_FORMAT_PROPERTY from the given Configuration.
protected	VCFOutputFormat(VCFFormat fmt) Creates a new output format for the given VCF format.

Method Summary

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

checkOutputSpecs, getCompressOutput, getDefaultWorkFile, getOutputCommitter, getOutputCompressorClass, getOutputName, getOutputPath, getPathForWorkFile, getRecordWriter, 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

OUTPUT_VCF_FORMAT_PROPERTY

public static final String OUTPUT_VCF_FORMAT_PROPERTY

A string property defining the output format to use. The value is read directly by VCFFormat.valueOf(java.lang.String).

See Also:

Constant Field Values

format

protected VCFFormat format

Constructor Detail

VCFOutputFormat

protected VCFOutputFormat(org.apache.hadoop.conf.Configuration conf)

Creates a new output format, reading OUTPUT_VCF_FORMAT_PROPERTY from the given Configuration.

VCFOutputFormat

protected VCFOutputFormat(VCFFormat fmt)

Creates a new output format for the given VCF format.