org.seqdoop.hadoop_bam

Class KeyIgnoringCRAMOutputFormat<K>

java.lang.Object

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

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

org.seqdoop.hadoop_bam.CRAMOutputFormat<K>

org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat<K>

public class KeyIgnoringCRAMOutputFormat<K>
extends CRAMOutputFormat<K>

Writes only the BAM records, not the key.

A SAMFileHeader must be provided via setSAMHeader(htsjdk.samtools.SAMFileHeader) or readSAMHeaderFrom(org.apache.hadoop.fs.Path, org.apache.hadoop.conf.Configuration) before getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext) is called.

By default, writes the SAM header to the output file(s). This can be disabled, because in distributed usage one often ends up with (and, for decent performance, wants to end up with) the output split into multiple parts, which are easier to concatenate if the header is not present in each file.

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 htsjdk.samtools.SAMFileHeader	header

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
KeyIgnoringCRAMOutputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordWriter<K,SAMRecordWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx) setSAMHeader or readSAMHeaderFrom must have been called first.
org.apache.hadoop.mapreduce.RecordWriter<K,SAMRecordWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx, org.apache.hadoop.fs.Path out)
htsjdk.samtools.SAMFileHeader	getSAMHeader()
boolean	getWriteHeader() Whether the header will be written or not.
void	readSAMHeaderFrom(InputStream in, org.apache.hadoop.conf.Configuration conf)
void	readSAMHeaderFrom(org.apache.hadoop.fs.Path path, org.apache.hadoop.conf.Configuration conf)
void	setSAMHeader(htsjdk.samtools.SAMFileHeader header)
void	setWriteHeader(boolean b) Set whether the header will be written or not.

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

checkOutputSpecs, 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

header

protected htsjdk.samtools.SAMFileHeader header

Constructor Detail

KeyIgnoringCRAMOutputFormat

public KeyIgnoringCRAMOutputFormat()

Method Detail

getWriteHeader

public boolean getWriteHeader()

Whether the header will be written or not.

setWriteHeader

public void setWriteHeader(boolean b)

Set whether the header will be written or not.

getSAMHeader

public htsjdk.samtools.SAMFileHeader getSAMHeader()

setSAMHeader

public void setSAMHeader(htsjdk.samtools.SAMFileHeader header)

readSAMHeaderFrom

public void readSAMHeaderFrom(org.apache.hadoop.fs.Path path,
                              org.apache.hadoop.conf.Configuration conf)
                       throws IOException

Throws:

IOException

readSAMHeaderFrom

public void readSAMHeaderFrom(InputStream in,
                              org.apache.hadoop.conf.Configuration conf)

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<K,SAMRecordWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                                                                              throws IOException

setSAMHeader or readSAMHeaderFrom must have been called first.

Specified by:

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

Throws:

IOException

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<K,SAMRecordWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
                                                                                     org.apache.hadoop.fs.Path out)
                                                                              throws IOException

Throws:

IOException