org.seqdoop.hadoop_bam

Class KeyIgnoringAnySAMOutputFormat<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>

org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat<K>

public class KeyIgnoringAnySAMOutputFormat<K>
extends AnySAMOutputFormat<K>

Writes only the SAM 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
static String	WRITE_HEADER_PROPERTY Whether the header will be written, defaults to true.

Fields inherited from class org.seqdoop.hadoop_bam.AnySAMOutputFormat

format, OUTPUT_SAM_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
KeyIgnoringAnySAMOutputFormat(org.apache.hadoop.conf.Configuration conf)
KeyIgnoringAnySAMOutputFormat(org.apache.hadoop.conf.Configuration conf, org.apache.hadoop.fs.Path path)
KeyIgnoringAnySAMOutputFormat(SAMFormat fmt)

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() Deprecated.
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) Deprecated.

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

WRITE_HEADER_PROPERTY

public static final String WRITE_HEADER_PROPERTY

Whether the header will be written, defaults to true. If set, overrides the deprecated setWriteHeader() setting.

See Also:

Constant Field Values

Constructor Detail

KeyIgnoringAnySAMOutputFormat

public KeyIgnoringAnySAMOutputFormat(SAMFormat fmt)

KeyIgnoringAnySAMOutputFormat

public KeyIgnoringAnySAMOutputFormat(org.apache.hadoop.conf.Configuration conf)

KeyIgnoringAnySAMOutputFormat

public KeyIgnoringAnySAMOutputFormat(org.apache.hadoop.conf.Configuration conf,
                                     org.apache.hadoop.fs.Path path)

Method Detail

getWriteHeader

@Deprecated
public boolean getWriteHeader()

Deprecated.

Whether the header will be written or not. Deprecated: use your Configuration and get WRITE_HEADER_PROPERTY instead.

setWriteHeader

@Deprecated
public void setWriteHeader(boolean b)

Deprecated.

Set whether the header will be written or not. Deprecated: use your Configuration and set WRITE_HEADER_PROPERTY instead.

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