SAMHeaderHadoopUtils (Eoulsan 2.6.1 API)

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

All Methods Static Methods Concrete Methods
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SAMHeaderHadoopUtils
```
public SAMHeaderHadoopUtils()
```
- Method Detail
  - 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