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

Class CompressedSplitFastqLineReader

java.lang.Object
org.apache.hadoop.util.LineReader
org.apache.hadoop.mapreduce.lib.input.SplitLineReader
fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
All Implemented Interfaces:
Closeable, AutoCloseable
public class CompressedSplitFastqLineReader extends org.apache.hadoop.mapreduce.lib.input.SplitLineReader
This class define a split line reader for compressed FASTQ files.
Since:
2.0
Author:
Laurent Jourdren

  • Constructor Summary

    Constructors
    Constructor
    Description
    CompressedSplitFastqLineReader(org.apache.hadoop.io.compress.SplitCompressionInputStream in, org.apache.hadoop.conf.Configuration conf, byte[] recordDelimiterBytes)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    needAdditionalRecordAfterSplit()
     
    int
    readLine(org.apache.hadoop.io.Text str, int maxLineLength, int maxBytesToConsume)
     

    Methods inherited from class org.apache.hadoop.util.LineReader

    close, readLine, readLine

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • CompressedSplitFastqLineReader

      public CompressedSplitFastqLineReader(org.apache.hadoop.io.compress.SplitCompressionInputStream in, org.apache.hadoop.conf.Configuration conf, byte[] recordDelimiterBytes) throws IOException
      Constructor.
      Parameters:
      in - input stream
      conf - Hadoop configuration
      recordDelimiterBytes - bytes
      Throws:
      IOException - if an error occurs while reading data

  • Method Details

    • readLine

      public int readLine(org.apache.hadoop.io.Text str, int maxLineLength, int maxBytesToConsume) throws IOException
      Overrides:
      readLine in class org.apache.hadoop.util.LineReader
      Throws:
      IOException

    • needAdditionalRecordAfterSplit

      public boolean needAdditionalRecordAfterSplit()
      Overrides:
      needAdditionalRecordAfterSplit in class org.apache.hadoop.mapreduce.lib.input.SplitLineReader