Class PreTreatmentReducer


  • public class PreTreatmentReducer
    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 reads filtering 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
    • Constructor Detail

      • PreTreatmentReducer

        public PreTreatmentReducer()
    • 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 read without the integer indicating the member of the pair. 'values': the rest of the paired TFQ lines (the member '1' and then the member '2').
        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