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.InterleavedFastqInputFormat

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

  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.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

    All Methods Instance Methods Concrete 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)` Creates the new record reader that underlies this input format.

    - ### 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, 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`

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