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