Class SingleFastqInputFormat


  • public final class SingleFastqInputFormat
    extends FastqInputFormat
    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
    • 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_NONRECURSIVE_IGNORE_SUBDIRS, INPUT_DIR_RECURSIVE, LIST_STATUS_NUM_THREADS, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE
    • 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.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
    • 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
        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