org.seqdoop.hadoop_bam

Class QseqOutputFormat

java.lang.Object

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

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

org.apache.hadoop.mapreduce.lib.output.TextOutputFormat<org.apache.hadoop.io.Text,SequencedFragment>

org.seqdoop.hadoop_bam.QseqOutputFormat

public class QseqOutputFormat
extends org.apache.hadoop.mapreduce.lib.output.TextOutputFormat<org.apache.hadoop.io.Text,SequencedFragment>

Output format for Illumina qseq format. Records are lines of tab-separated fields. Each record consists of - Machine name - Run number - Lane number - Tile number - X coordinate of the spot. Integer (can be negative). - Y coordinate of the spot. Integer (can be negative). - Index - Read Number - Sequence - Quality - Filter

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	QseqOutputFormat.QseqRecordWriter

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.output.TextOutputFormat

org.apache.hadoop.mapreduce.lib.output.TextOutputFormat.LineRecordWriter<K,V>

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	CONF_BASE_QUALITY_ENCODING
static String	CONF_BASE_QUALITY_ENCODING_DEFAULT

Fields inherited from class org.apache.hadoop.mapreduce.lib.output.TextOutputFormat

SEPERATOR

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
QseqOutputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext task)

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

CONF_BASE_QUALITY_ENCODING

public static final String CONF_BASE_QUALITY_ENCODING

See Also:

Constant Field Values

CONF_BASE_QUALITY_ENCODING_DEFAULT

public static final String CONF_BASE_QUALITY_ENCODING_DEFAULT

See Also:

Constant Field Values

Constructor Detail

QseqOutputFormat

public QseqOutputFormat()

Method Detail

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext task)
                                                                                                      throws IOException

Overrides:

getRecordWriter in class org.apache.hadoop.mapreduce.lib.output.TextOutputFormat<org.apache.hadoop.io.Text,SequencedFragment>

Throws:

IOException