ReferenceSource (htsjdk 2.5.0 API)

java.lang.Object
- htsjdk.samtools.cram.ref.ReferenceSource

All Implemented Interfaces:

CRAMReferenceSource
```
public class ReferenceSource
extends java.lang.Object
implements CRAMReferenceSource
```
Used to represent a CRAM reference, the backing source for which can either be a file or the EBI ENA reference service. NOTE: In a future release, this class will be renamed and the functionality it contains will be refactored and distributed into one or more separate reference source implementations, each corresponding to the type of resource backing the reference.

Constructor Summary

Constructors
Constructor and Description

ReferenceSource(java.io.File file)

ReferenceSource(java.nio.file.Path path)

ReferenceSource(ReferenceSequenceFile rsFile)

Constructors
Constructor and Description
`ReferenceSource(java.io.File file)`
`ReferenceSource(java.nio.file.Path path)`
`ReferenceSource(ReferenceSequenceFile rsFile)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clearCache()`
`static CRAMReferenceSource`	`getDefaultCRAMReferenceSource()` Attempts to construct a default CRAMReferenceSource for use with CRAM files when one has not been explicitly provided.
`int`	`getDownloadTriesBeforeFailing()`
`byte[]`	`getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants)` getReferenceBases
`void`	`setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ReferenceSource
```
public ReferenceSource(java.io.File file)
```
  - ReferenceSource
```
public ReferenceSource(java.nio.file.Path path)
```
  - ReferenceSource
```
public ReferenceSource(ReferenceSequenceFile rsFile)
```
- Method Detail
  - getDefaultCRAMReferenceSource
```
public static CRAMReferenceSource getDefaultCRAMReferenceSource()
```
    Attempts to construct a default CRAMReferenceSource for use with CRAM files when one has not been explicitly provided.
    Returns:
    
    CRAMReferenceSource if one can be acquired. Guaranteed to not be null if none of the listed exceptions is thrown.
    
    Throws:
    
    java.lang.IllegalStateException - if no default reference source can be acquired
    java.lang.IllegalArgumentException - if the reference_fasta environment variable refers to a a file that doesn't exist
    Construct a default reference source to use when an explicit reference has not been provided by checking for fallback sources in this order:
    
    Defaults.REFERENCE_FASTA - the value of the system property "reference_fasta". If set, must refer to a valid reference file.
    
    ENA Reference Service if it is enabled
  - clearCache
```
public void clearCache()
```
  - getReferenceBases
```
public byte[] getReferenceBases(SAMSequenceRecord record,
                                boolean tryNameVariants)
```
    Description copied from interface: CRAMReferenceSource
    
    getReferenceBases
    
    Specified by:
    
    getReferenceBases in interface CRAMReferenceSource
    
    Parameters:
    
    record - the SAMSequenceRecord identifying the reference being requested
    
    tryNameVariants - if true, attempt to match the requested sequence name against the reference by using common name variations, such as adding or removing a leading "chr" prefix from the requested name. if false, use exact match
    
    Returns:
    
    the bases representing the requested sequence. or null if the sequence cannot be found
  - getDownloadTriesBeforeFailing
```
public int getDownloadTriesBeforeFailing()
```
  - setDownloadTriesBeforeFailing
```
public void setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)
```

Class ReferenceSource

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ReferenceSource

ReferenceSource

ReferenceSource

Method Detail

getDefaultCRAMReferenceSource

clearCache

getReferenceBases

getDownloadTriesBeforeFailing

setDownloadTriesBeforeFailing