Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Class SAMHeaderHadoopUtils.SAMHeaderWriter

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter

Enclosing class:

SAMHeaderHadoopUtils

public static class SAMHeaderHadoopUtils.SAMHeaderWriter
extends Object

This class allow to save the SAM header read by a mapper.

Constructor Summary

Constructors

Constructor	Description
SAMHeaderWriter(String attemptId)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	close(org.apache.hadoop.mapreduce.JobContext context)	Close the SAM file header.
boolean	writeIfHeaderLine(org.apache.hadoop.mapreduce.JobContext context, String line)	Write the line to the SAM header file if the line is a SAM header.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SAMHeaderWriter

public SAMHeaderWriter(String attemptId)

Constructor.

Parameters:

attemptId - Hadoop task attempt Id

Method Detail

writeIfHeaderLine

public boolean writeIfHeaderLine(org.apache.hadoop.mapreduce.JobContext context,
                                 String line)
                          throws IOException

Write the line to the SAM header file if the line is a SAM header.

Parameters:

context - the Hadoop context

line - the line read

Returns:

if the line is an header or an empty line

Throws:

IOException - if an error occurs while writing the SAM file header

close

public void close(org.apache.hadoop.mapreduce.JobContext context)
           throws IOException

Close the SAM file header.

Parameters:

context - the Hadoop context

Throws:

IOException - if an error occurs while writing the SAM file header