htsjdk.samtools

Class SamReaderFactory

java.lang.Object

htsjdk.samtools.SamReaderFactory

public abstract class SamReaderFactory
extends java.lang.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 and Description
static class	SamReaderFactory.Option A collection of binary SamReaderFactory options.

Constructor Summary

Constructors

Constructor and Description
SamReaderFactory()

Method Summary

Modifier and Type	Method and 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(java.io.File samFile) Utility method to open the file get the header and close the file
abstract SAMFileHeader	getFileHeader(java.nio.file.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(java.io.File file)
SamReader	open(java.nio.file.Path path) Open the specified path (without using any wrappers).
SamReader	open(java.nio.file.Path path, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> dataWrapper, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper) Open the specified path, using the specified wrappers for prefetching/caching.
abstract SamReader	open(SamInputResource resource)
abstract void	reapplyOptions(SamReader reader) Reapplies any changed options to the reader *
abstract SamReaderFactory	referenceSequence(java.io.File referenceSequence) Sets the specified reference sequence *
abstract SamReaderFactory	referenceSequence(java.nio.file.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(java.io.File file)

open

public SamReader open(java.nio.file.Path path)

Open the specified path (without using any wrappers).

Parameters:

path - the SAM or BAM file to open.

open

public SamReader open(java.nio.file.Path path,
                      java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> dataWrapper,
                      java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.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(java.io.File referenceSequence)

Sets the specified reference sequence *

referenceSequence

public abstract SamReaderFactory referenceSequence(java.nio.file.Path referenceSequence)

Sets the specified reference sequence.

referenceSource

public abstract SamReaderFactory referenceSource(CRAMReferenceSource referenceSequence)

Sets the specified reference sequence *

getFileHeader

public abstract SAMFileHeader getFileHeader(java.io.File samFile)

Utility method to open the file get the header and close the file

getFileHeader

public abstract SAMFileHeader getFileHeader(java.nio.file.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.