org.seqdoop.hadoop_bam

Class AnySAMOutputFormat<K>

java.lang.Object

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

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

org.seqdoop.hadoop_bam.AnySAMOutputFormat<K>

Direct Known Subclasses:

KeyIgnoringAnySAMOutputFormat

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

An abstract OutputFormat for SAM and BAM 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 SAMFormat	format
static String	OUTPUT_SAM_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	AnySAMOutputFormat(org.apache.hadoop.conf.Configuration conf) Creates a new output format, reading OUTPUT_SAM_FORMAT_PROPERTY from the given Configuration.
protected	AnySAMOutputFormat(SAMFormat fmt) Creates a new output format for the given SAM 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_SAM_FORMAT_PROPERTY

public static final String OUTPUT_SAM_FORMAT_PROPERTY

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

See Also:

Constant Field Values

format

protected SAMFormat format

Constructor Detail

AnySAMOutputFormat

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

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

AnySAMOutputFormat

protected AnySAMOutputFormat(SAMFormat fmt)

Creates a new output format for the given SAM format.