org.bdgenomics.adam.io

Class InterleavedFastqInputFormat

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.FastqInputFormat

org.bdgenomics.adam.io.InterleavedFastqInputFormat

public final class InterleavedFastqInputFormat
extends FastqInputFormat

This class is a Hadoop reader for "interleaved fastq" -- that is, fastq with paired reads in the same file, interleaved, rather than in two separate files. This makes it much easier to Hadoopily slice up a single file and feed the slices into an aligner. The format is the same as fastq, but records are expected to alternate between /1 and /2. As a precondition, we assume that the interleaved FASTQ files are always uncompressed; if the files are compressed, they cannot be split, and thus there is no reason to use the interleaved format. 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

Nested Class Summary

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.bdgenomics.adam.io.FastqInputFormat

splittable

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

DEFAULT_LIST_STATUS_NUM_THREADS, INPUT_DIR, INPUT_DIR_RECURSIVE, LIST_STATUS_NUM_THREADS, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

Constructor Summary

Constructors

Constructor and Description
InterleavedFastqInputFormat()

Method Summary

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) Creates the new record reader that underlies this input format.

Methods inherited from class org.bdgenomics.adam.io.FastqInputFormat

isSplitable

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, 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

InterleavedFastqInputFormat

public InterleavedFastqInputFormat()

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

Creates the new record reader that underlies this input format.

Specified by:

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

Parameters:

genericSplit - The split that the record reader should read.

context - The Hadoop task context.

Returns:

Returns the interleaved FASTQ record reader.

Throws:

IOException

InterruptedException