org.bdgenomics.adam.io

Class SingleFastqInputFormat

java.lang.Object

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

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

org.bdgenomics.adam.io.SingleFastqInputFormat

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

This class is a Hadoop reader for single read fastq. This reader is based on the FastqInputFormat that's part of Hadoop-BAM, found at https://github.com/HadoopGenomics/Hadoop-BAM/blob/master/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java

Author:

Frank Austin Nothaft (fnothaft@berkeley.edu)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SingleFastqInputFormat.SingleFastqRecordReader

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

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

Field Summary

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
SingleFastqInputFormat()

Method Summary

Methods

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)

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

addInputPath, addInputPathRecursively, addInputPaths, computeSplitSize, getBlockIndex, getFormatMinSplitSize, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, getSplits, isSplitable, 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

Constructor Detail

SingleFastqInputFormat

public SingleFastqInputFormat()

Method Detail

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text> 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<Void,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException