Class PreTreatmentExpressionReducer


  • public class PreTreatmentExpressionReducer
    extends org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text>
    This class define a reducer for the pretreatment of paired-end data before the expression estimation step.
    Since:
    1.2
    Author:
    Claire Wallon
    • Nested Class Summary

      • Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.Reducer

        org.apache.hadoop.mapreduce.Reducer.Context
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void reduce​(org.apache.hadoop.io.Text key, Iterable<org.apache.hadoop.io.Text> values, org.apache.hadoop.mapreduce.Reducer.Context context)
      'key': the identifier of the aligned read without the integer indicating the member of the pair.
      protected void setup​(org.apache.hadoop.mapreduce.Reducer.Context context)  
      • Methods inherited from class org.apache.hadoop.mapreduce.Reducer

        cleanup, run
    • Constructor Detail

      • PreTreatmentExpressionReducer

        public PreTreatmentExpressionReducer()
    • Method Detail

      • setup

        protected void setup​(org.apache.hadoop.mapreduce.Reducer.Context context)
                      throws IOException,
                             InterruptedException
        Overrides:
        setup in class org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text>
        Throws:
        IOException
        InterruptedException
      • reduce

        protected void reduce​(org.apache.hadoop.io.Text key,
                              Iterable<org.apache.hadoop.io.Text> values,
                              org.apache.hadoop.mapreduce.Reducer.Context context)
                       throws IOException,
                              InterruptedException
        'key': the identifier of the aligned read without the integer indicating the member of the pair. 'values': the rest of the paired alignments, i.e the SAM line of the first paired alignment and the SAM line of the second paired alignment.
        Overrides:
        reduce in class org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text>
        Throws:
        IOException
        InterruptedException