Class ExpressionMapper


  • public class ExpressionMapper
    extends org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.LongWritable>
    Mapper for the expression estimation.
    Since:
    1.2
    Author:
    Claire Wallon
    • Nested Class Summary

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

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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void cleanup​(org.apache.hadoop.mapreduce.Mapper.Context context)  
      void map​(org.apache.hadoop.io.Text key, org.apache.hadoop.io.Text value, org.apache.hadoop.mapreduce.Mapper.Context context)
      'key': offset of the beginning of the line from the beginning of the alignment file.
      void setup​(org.apache.hadoop.mapreduce.Mapper.Context context)  
      • Methods inherited from class org.apache.hadoop.mapreduce.Mapper

        run
    • Constructor Detail

      • ExpressionMapper

        public ExpressionMapper()
    • Method Detail

      • setup

        public void setup​(org.apache.hadoop.mapreduce.Mapper.Context context)
                   throws IOException,
                          InterruptedException
        Overrides:
        setup in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.LongWritable>
        Throws:
        IOException
        InterruptedException
      • map

        public void map​(org.apache.hadoop.io.Text key,
                        org.apache.hadoop.io.Text value,
                        org.apache.hadoop.mapreduce.Mapper.Context context)
                 throws IOException,
                        InterruptedException
        'key': offset of the beginning of the line from the beginning of the alignment file. 'value': the SAM record, if data are in paired-end mode, 'value' contains the two paired alignments separated by a '£' (TSAM format).
        Overrides:
        map in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.LongWritable>
        Throws:
        IOException
        InterruptedException
      • cleanup

        public void cleanup​(org.apache.hadoop.mapreduce.Mapper.Context context)
                     throws IOException
        Overrides:
        cleanup in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.Text,​org.apache.hadoop.io.LongWritable>
        Throws:
        IOException