java.lang.Object
- htsjdk.samtools.SamReaderFactory

public abstract class SamReaderFactory
extends Object

Describes the functionality for producing SamReader, and offers a handful of static generators.

     SamReaderFactory.makeDefault().open(new File("/my/bam.bam");

Example: Configure a factory

      final SamReaderFactory factory =
          SamReaderFactory.makeDefault()
              .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
              .validationStringency(ValidationStringency.SILENT);

Example: Open two bam files from different sources, using different options

     final SamReaderFactory factory =
          SamReaderFactory.makeDefault()
              .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
              .validationStringency(ValidationStringency.SILENT);

     // File-based bam
     final SamReader fileReader = factory.open(new File("/my/bam.bam"));

     // HTTP-hosted BAM with index from an arbitrary stream
     final SeekableStream myBamIndexStream = ...
     final SamInputResource resource =
          SamInputResource.of(new URL("http://example.com/data.bam")).index(myBamIndexStream);
     final SamReader complicatedReader = factory.open(resource);

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class SamReaderFactory.Option
A collection of binary SamReaderFactory options.

Constructor Summary

Constructors
Constructor Description

SamReaderFactory()

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract SamReaderFactory`	`disable(SamReaderFactory.Option... options)`	Disables the provided `SamReaderFactory.Option`s, then returns itself.
`abstract SamReaderFactory`	`enable(SamReaderFactory.Option... options)`	Enables the provided `SamReaderFactory.Option`s, then returns itself.
`abstract SAMFileHeader`	`getFileHeader(File samFile)`	Utility method to open the file get the header and close the file
`abstract SAMFileHeader`	`getFileHeader(Path samFile)`	Utility method to open the file get the header and close the file
`abstract SamReaderFactory`	`inflaterFactory(InflaterFactory inflaterFactory)`	Set this factory's `InflaterFactory` to the provided one, then returns itself.
`static SamReaderFactory`	`make()`	Creates an "empty" factory with no enabled `SamReaderFactory.Option`s, `ValidationStringency.DEFAULT_STRINGENCY`, no path wrapper, and `DefaultSAMRecordFactory`.
`static SamReaderFactory`	`makeDefault()`	Creates a copy of the default `SamReaderFactory`.
`abstract SamReader`	`open(SamInputResource resource)`
`abstract SamReader`	`open(File file)`
`SamReader`	`open(Path path)`	Open the specified path (without using any wrappers).
`SamReader`	`open(Path path, Function<SeekableByteChannel,SeekableByteChannel> dataWrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)`	Open the specified path, using the specified wrappers for prefetching/caching.
`abstract void`	`reapplyOptions(SamReader reader)`	Reapplies any changed options to the reader *
`abstract SamReaderFactory`	`referenceSequence(File referenceSequence)`	Sets the specified reference sequence *
`abstract SamReaderFactory`	`referenceSequence(Path referenceSequence)`	Sets the specified reference sequence.
`abstract CRAMReferenceSource`	`referenceSource()`
`abstract SamReaderFactory`	`referenceSource(CRAMReferenceSource referenceSequence)`	Sets the specified reference sequence *
`abstract SamReaderFactory`	`samRecordFactory(SAMRecordFactory samRecordFactory)`	Set this factory's `SAMRecordFactory` to the provided one, then returns itself.
`static void`	`setDefaultValidationStringency(ValidationStringency defaultValidationStringency)`
`abstract SamReaderFactory`	`setOption(SamReaderFactory.Option option, boolean value)`	Sets a specific Option to a boolean value.
`abstract SamReaderFactory`	`setUseAsyncIo(boolean asynchronousIO)`	Set whether readers created by this factory will use asynchronous IO.
`abstract ValidationStringency`	`validationStringency()`
`abstract SamReaderFactory`	`validationStringency(ValidationStringency validationStringency)`	Set this factory's `ValidationStringency` to the provided one, then returns itself.

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

- Constructor Detail
  - SamReaderFactory
```
public SamReaderFactory()
```
- Method Detail
  - open
```
public abstract SamReader open(File file)
```
  - open
```
public SamReader open(Path path)
```
    Open the specified path (without using any wrappers).
    
    Parameters:
    
    path - the SAM or BAM file to open.
  - open
```
public SamReader open(Path path,
                      Function<SeekableByteChannel,SeekableByteChannel> dataWrapper,
                      Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
```
    Open the specified path, using the specified wrappers for prefetching/caching.
    
    Parameters:
    
    path - the SAM or BAM file to open
    
    dataWrapper - the wrapper for the data (or null for none)
    
    indexWrapper - the wrapper for the index (or null for none)
  - open
```
public abstract SamReader open(SamInputResource resource)
```
  - validationStringency
```
public abstract ValidationStringency validationStringency()
```
  - referenceSource
```
public abstract CRAMReferenceSource referenceSource()
```
  - samRecordFactory
```
public abstract SamReaderFactory samRecordFactory(SAMRecordFactory samRecordFactory)
```
    Set this factory's SAMRecordFactory to the provided one, then returns itself.
  - inflaterFactory
```
public abstract SamReaderFactory inflaterFactory(InflaterFactory inflaterFactory)
```
    Set this factory's InflaterFactory to the provided one, then returns itself. Note: The inflaterFactory provided here is only used for BAM decompression implemented with BAMFileReader, it is not used for CRAM or other formats like a gzipped SAM file.
  - enable
```
public abstract SamReaderFactory enable(SamReaderFactory.Option... options)
```
    Enables the provided SamReaderFactory.Options, then returns itself.
  - disable
```
public abstract SamReaderFactory disable(SamReaderFactory.Option... options)
```
    Disables the provided SamReaderFactory.Options, then returns itself.
  - setOption
```
public abstract SamReaderFactory setOption(SamReaderFactory.Option option,
                                           boolean value)
```
    Sets a specific Option to a boolean value. *
  - referenceSequence
```
public abstract SamReaderFactory referenceSequence(File referenceSequence)
```
    Sets the specified reference sequence *
  - referenceSequence
```
public abstract SamReaderFactory referenceSequence(Path referenceSequence)
```
    Sets the specified reference sequence.
  - referenceSource
```
public abstract SamReaderFactory referenceSource(CRAMReferenceSource referenceSequence)
```
    Sets the specified reference sequence *
  - getFileHeader
```
public abstract SAMFileHeader getFileHeader(File samFile)
```
    Utility method to open the file get the header and close the file
  - getFileHeader
```
public abstract SAMFileHeader getFileHeader(Path samFile)
```
    Utility method to open the file get the header and close the file
  - reapplyOptions
```
public abstract void reapplyOptions(SamReader reader)
```
    Reapplies any changed options to the reader *
  - validationStringency
```
public abstract SamReaderFactory validationStringency(ValidationStringency validationStringency)
```
    Set this factory's ValidationStringency to the provided one, then returns itself.
  - setUseAsyncIo
```
public abstract SamReaderFactory setUseAsyncIo(boolean asynchronousIO)
```
    Set whether readers created by this factory will use asynchronous IO. If this methods is not called, this flag will default to the value of Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS. Note that this option may not be applicable to all readers returned from this factory. Returns the factory itself.
  - setDefaultValidationStringency
```
public static void setDefaultValidationStringency(ValidationStringency defaultValidationStringency)
```
  - makeDefault
```
public static SamReaderFactory makeDefault()
```
    Creates a copy of the default SamReaderFactory.
  - make
```
public static SamReaderFactory make()
```
    Creates an "empty" factory with no enabled SamReaderFactory.Options, ValidationStringency.DEFAULT_STRINGENCY, no path wrapper, and DefaultSAMRecordFactory.

Class SamReaderFactory

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SamReaderFactory

Method Detail

open

open

open

open

validationStringency

referenceSource

samRecordFactory

inflaterFactory

enable

disable

setOption

referenceSequence

referenceSequence

referenceSource

getFileHeader

getFileHeader

reapplyOptions

validationStringency

setUseAsyncIo

setDefaultValidationStringency

makeDefault

make