Package org.bdgenomics.adam.io
Class InterleavedFastqInputFormat
- java.lang.Object
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- org.apache.hadoop.mapreduce.InputFormat<K,V>
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- org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>
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- org.bdgenomics.adam.io.FastqInputFormat
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- org.bdgenomics.adam.io.InterleavedFastqInputFormat
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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
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Field Summary
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Fields inherited from class org.bdgenomics.adam.io.FastqInputFormat
splittable
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Constructor Summary
Constructors Constructor Description InterleavedFastqInputFormat()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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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
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Method Detail
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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 classorg.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
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