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

Class SAMHeaderHadoopUtils

java.lang.Object

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

public class SAMHeaderHadoopUtils
extends Object

This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.

Since:

2.0

Author:

Laurent Jourdren

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SAMHeaderHadoopUtils.SAMHeaderWriter	This class allow to save the SAM header read by a mapper.

Constructor Summary

Constructors

Constructor	Description
SAMHeaderHadoopUtils()

Method Summary

Modifier and Type	Method	Description
static htsjdk.samtools.SAMSequenceDictionary	createSAMSequenceDictionaryFromSAMHeader(List<String> headers)	Create a SAMSequenceDictionary from the SAM header in a list of String.
static List<String>	loadSAMHeaders(org.apache.hadoop.mapreduce.JobContext context)	Load SAM headers.

Methods inherited from class java.lang.Object

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

Constructor Details

SAMHeaderHadoopUtils

public SAMHeaderHadoopUtils()

Method Details

loadSAMHeaders

public static List<String> loadSAMHeaders(org.apache.hadoop.mapreduce.JobContext context)
                                   throws IOException

Load SAM headers.

Parameters:

context - the Hadoop context

Returns:

a list of String with the SAM headers

Throws:

IOException - if an error occurs while loading the headers

createSAMSequenceDictionaryFromSAMHeader

public static htsjdk.samtools.SAMSequenceDictionary createSAMSequenceDictionaryFromSAMHeader(List<String> headers)

Create a SAMSequenceDictionary from the SAM header in a list of String.

Parameters:

headers - the list of String

Returns:

a new SAMSequenceDictionary object with the SAM headers