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 enum

SamReaderFactory.Option

A collection of binary SamReaderFactory options.
Constructor Summary

Constructors

Constructor

Description

SamReaderFactory()
Method Summary

Modifier and Type

Method

Description

abstract SamReaderFactory

disable(SamReaderFactory.Option... options)

Disables the provided SamReaderFactory.Options, then returns itself.

abstract SamReaderFactory

enable(SamReaderFactory.Option... options)

Enables the provided SamReaderFactory.Options, 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.Options, 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 Details
- SamReaderFactory
  
  public SamReaderFactory()
Method Details
- 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 Details

SamReaderFactory

Method Details

open

open

open

open

validationStringency

referenceSource

samRecordFactory

inflaterFactory

enable

disable

setOption

referenceSequence

referenceSequence

referenceSource

getFileHeader

getFileHeader

reapplyOptions

validationStringency

setUseAsyncIo

setDefaultValidationStringency

makeDefault

make