org.seqdoop.hadoop_bam

Class FastqOutputFormat.FastqRecordWriter

java.lang.Object

org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>

org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter

Enclosing class:

FastqOutputFormat

public static class FastqOutputFormat.FastqRecordWriter
extends org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>

Field Summary

Fields

Modifier and Type	Field and Description
protected FormatConstants.BaseQualityEncoding	baseQualityFormat
protected org.apache.hadoop.io.Text	buffer
protected OutputStream	out
protected StringBuilder	sBuilder

Constructor Summary

Constructors

Constructor and Description
FastqRecordWriter(org.apache.hadoop.conf.Configuration conf, OutputStream out)

Method Summary

Modifier and Type	Method and Description
void	close(org.apache.hadoop.mapreduce.TaskAttemptContext task)
protected String	makeId(SequencedFragment seq)
void	setConf(org.apache.hadoop.conf.Configuration conf)
void	write(org.apache.hadoop.io.Text key, SequencedFragment seq)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sBuilder

protected StringBuilder sBuilder

buffer

protected org.apache.hadoop.io.Text buffer

out

protected OutputStream out

baseQualityFormat

protected FormatConstants.BaseQualityEncoding baseQualityFormat

Constructor Detail

FastqRecordWriter

public FastqRecordWriter(org.apache.hadoop.conf.Configuration conf,
                         OutputStream out)

Method Detail

setConf

public void setConf(org.apache.hadoop.conf.Configuration conf)

makeId

protected String makeId(SequencedFragment seq)
                 throws IOException

Throws:

IOException

write

public void write(org.apache.hadoop.io.Text key,
                  SequencedFragment seq)
           throws IOException

Specified by:

write in class org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>

Throws:

IOException

close

public void close(org.apache.hadoop.mapreduce.TaskAttemptContext task)
           throws IOException

Specified by:

close in class org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>

Throws:

IOException