org.seqdoop.hadoop_bam

Class QseqInputFormat

java.lang.Object

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

org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,SequencedFragment>

org.seqdoop.hadoop_bam.QseqInputFormat

public class QseqInputFormat
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,SequencedFragment>

Reads the Illumina qseq sequence format. Key: instrument, run number, lane, tile, xpos, ypos, read number, delimited by ':' characters. Value: a SequencedFragment object representing the entry.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	QseqInputFormat.QseqRecordReader

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

org.apache.hadoop.mapreduce.lib.input.FileInputFormat.Counter

Field Summary

Fields

Modifier and Type	Field and Description
static String	CONF_BASE_QUALITY_ENCODING
static String	CONF_BASE_QUALITY_ENCODING_DEFAULT
static String	CONF_FILTER_FAILED_QC

Fields inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

INPUT_DIR, INPUT_DIR_RECURSIVE, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

Constructor Summary

Constructors

Constructor and Description
QseqInputFormat()

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,SequencedFragment>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
boolean	isSplitable(org.apache.hadoop.mapreduce.JobContext context, org.apache.hadoop.fs.Path path)

Methods inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat

addInputPath, addInputPathRecursively, addInputPaths, computeSplitSize, getBlockIndex, getFormatMinSplitSize, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, getSplits, listStatus, makeSplit, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

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_FILTER_FAILED_QC

public static final String CONF_FILTER_FAILED_QC

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

QseqInputFormat

public QseqInputFormat()

Method Detail

isSplitable

public boolean isSplitable(org.apache.hadoop.mapreduce.JobContext context,
                           org.apache.hadoop.fs.Path path)

Overrides:

isSplitable in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,SequencedFragment>

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,SequencedFragment> createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit,
                                                                                                                org.apache.hadoop.mapreduce.TaskAttemptContext context)
                                                                                                         throws IOException,
                                                                                                                InterruptedException

Specified by:

createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<org.apache.hadoop.io.Text,SequencedFragment>

Throws:

IOException

InterruptedException