Class PreTreatmentExpressionReducer
- java.lang.Object
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- 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>
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- fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
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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
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Constructor Summary
Constructors Constructor Description PreTreatmentExpressionReducer()
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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)
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Method Detail
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setup
protected void setup(org.apache.hadoop.mapreduce.Reducer.Context context) throws IOException, InterruptedException
- Overrides:
setup
in classorg.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
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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 classorg.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
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