org.seqdoop.hadoop_bam

Class BAMOutputFormat<K>

java.lang.Object

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

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

org.seqdoop.hadoop_bam.BAMOutputFormat<K>

Direct Known Subclasses:

KeyIgnoringBAMOutputFormat

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

Currently this only locks down the value type of the OutputFormat: contains no functionality.

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 String	WRITE_SPLITTING_BAI If set to true, write .splitting-bai files for every BAM file (defaults to false).

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
BAMOutputFormat()

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

WRITE_SPLITTING_BAI

public static final String WRITE_SPLITTING_BAI

If set to true, write .splitting-bai files for every BAM file (defaults to false). A splitting BAI file (not to be confused with a regular BAI file) contains an index of offsets that the BAM file can be read from; they are used by BAMInputFormat to construct splits.

See Also:

Constant Field Values

Constructor Detail

BAMOutputFormat

public BAMOutputFormat()