|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object htsjdk.samtools.SamReaderFactory
public abstract class SamReaderFactory
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
finalSamReaderFactory
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
finalSamReaderFactory
factory = SamReaderFactory.makeDefault() .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS
,SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS
) .validationStringency(ValidationStringency.SILENT
); // File-based bam finalSamReader
fileReader = factory.open(new File("/my/bam.bam")); // HTTP-hosted BAM with index from an arbitrary stream final SeekableStream myBamIndexStream = ... finalSamInputResource
resource =SamInputResource
.of(new URL("http://example.com/data.bam")).index(myBamIndexStream); finalSamReader
complicatedReader = factory.open(resource);
Nested Class Summary | |
---|---|
static class |
SamReaderFactory.Option
A collection of binary SamReaderFactory options. |
Constructor Summary | |
---|---|
SamReaderFactory()
|
Method Summary | |
---|---|
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(java.io.File samFile)
Utility method to open the file get the header and close the file |
static SamReaderFactory |
make()
Creates an "empty" factory with no enabled SamReaderFactory.Option s, ValidationStringency.DEFAULT_STRINGENCY , and
DefaultSAMRecordFactory . |
static SamReaderFactory |
makeDefault()
Creates a copy of the default SamReaderFactory . |
abstract SamReader |
open(java.io.File file)
|
abstract SamReader |
open(SamInputResource resource)
|
abstract void |
reapplyOptions(SamReader reader)
Reapplies any changed options to the reader * |
abstract java.io.File |
referenceSequence()
|
abstract SamReaderFactory |
referenceSequence(java.io.File 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 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 |
---|
public SamReaderFactory()
Method Detail |
---|
public abstract SamReader open(java.io.File file)
public abstract SamReader open(SamInputResource resource)
public abstract ValidationStringency validationStringency()
public abstract java.io.File referenceSequence()
public abstract SamReaderFactory samRecordFactory(SAMRecordFactory samRecordFactory)
SAMRecordFactory
to the provided one, then returns itself.
public abstract SamReaderFactory enable(SamReaderFactory.Option... options)
SamReaderFactory.Option
s, then returns itself.
public abstract SamReaderFactory disable(SamReaderFactory.Option... options)
SamReaderFactory.Option
s, then returns itself.
public abstract SamReaderFactory setOption(SamReaderFactory.Option option, boolean value)
public abstract SamReaderFactory referenceSequence(java.io.File referenceSequence)
public abstract SAMFileHeader getFileHeader(java.io.File samFile)
public abstract void reapplyOptions(SamReader reader)
public abstract SamReaderFactory validationStringency(ValidationStringency validationStringency)
ValidationStringency
to the provided one, then returns itself.
public static void setDefaultValidationStringency(ValidationStringency defaultValidationStringency)
public static SamReaderFactory makeDefault()
SamReaderFactory
.
public static SamReaderFactory make()
SamReaderFactory.Option
s, ValidationStringency.DEFAULT_STRINGENCY
, and
DefaultSAMRecordFactory
.
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |