Package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop

Class SAMInputFormat

java.lang.Object
org.apache.hadoop.mapreduce.InputFormat<K,V>
org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>
fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
public class SAMInputFormat extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>
This class define an InputFormat for SAM files for the Hadoop MapReduce framework.
Since:
2.0
Author:
Laurent Jourdren

  • 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

    INPUT_DIR, INPUT_DIR_RECURSIVE, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

  • Constructor Summary

    Constructors
    Constructor
    Description
    SAMInputFormat()
     

  • Method Summary

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

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

    addInputPath, addInputPaths, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, getSplits, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • SAMInputFormat

      public SAMInputFormat()

  • Method Details

    • createRecordReader

      public org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text> createRecordReader(org.apache.hadoop.mapreduce.InputSplit inputSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context) throws IOException, InterruptedException
      Specified by:
      createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>
      Throws:
      IOException
      InterruptedException