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B

BaiWriteOption - Enum in org.disq_bio.disq

An option for for enabling or disabling writing BAI files.

BAM - org.disq_bio.disq.ReadsFormatWriteOption

BAM format

C

CraiWriteOption - Enum in org.disq_bio.disq

An option for for enabling or disabling writing CRAI files.

CRAM - org.disq_bio.disq.ReadsFormatWriteOption

CRAM format

D

DISABLE - org.disq_bio.disq.BaiWriteOption

DISABLE - org.disq_bio.disq.CraiWriteOption

DISABLE - org.disq_bio.disq.SbiWriteOption

DISABLE - org.disq_bio.disq.TabixIndexWriteOption

DisqKryoRegistrator - Class in org.disq_bio.disq.serializer

Kryo registrator for Disq.

DisqKryoRegistrator() - Constructor for class org.disq_bio.disq.serializer.DisqKryoRegistrator

E

ENABLE - org.disq_bio.disq.BaiWriteOption

ENABLE - org.disq_bio.disq.CraiWriteOption

ENABLE - org.disq_bio.disq.SbiWriteOption

ENABLE - org.disq_bio.disq.TabixIndexWriteOption

F

FileCardinalityWriteOption - Enum in org.disq_bio.disq

An option for configuring whether to write output in a single file, or multiple files.

fromBoolean(boolean) - Static method in enum org.disq_bio.disq.BaiWriteOption

Turn a boolean into a BaiWriteOption.

fromBoolean(boolean) - Static method in enum org.disq_bio.disq.CraiWriteOption

Turn a boolean into a CraiWriteOption.

fromBoolean(boolean) - Static method in enum org.disq_bio.disq.SbiWriteOption

Turn a boolean into a SbiWriteOption.

fromBoolean(boolean) - Static method in enum org.disq_bio.disq.TabixIndexWriteOption

Turn a boolean into a TabixIndexWriteOption.

G

getHeader() - Method in class org.disq_bio.disq.HtsjdkReadsRdd

getHeader() - Method in class org.disq_bio.disq.HtsjdkVariantsRdd

getIndexExtension() - Static method in enum org.disq_bio.disq.BaiWriteOption

getIndexExtension() - Static method in enum org.disq_bio.disq.CraiWriteOption

getIndexExtension() - Static method in enum org.disq_bio.disq.SbiWriteOption

getIndexExtension() - Static method in enum org.disq_bio.disq.TabixIndexWriteOption

getIntervalsForTraversal() - Method in class org.disq_bio.disq.HtsjdkReadsTraversalParameters

getReads() - Method in class org.disq_bio.disq.HtsjdkReadsRdd

getTraverseUnplacedUnmapped() - Method in class org.disq_bio.disq.HtsjdkReadsTraversalParameters

getVariants() - Method in class org.disq_bio.disq.HtsjdkVariantsRdd

H

HtsjdkReadsRdd - Class in org.disq_bio.disq

A HtsjdkReadsRdd is the distributed equivalent of a htsjdk SamReader.

HtsjdkReadsRdd(SAMFileHeader, JavaRDD<SAMRecord>) - Constructor for class org.disq_bio.disq.HtsjdkReadsRdd

HtsjdkReadsRddStorage - Class in org.disq_bio.disq

The entry point for reading or writing a HtsjdkReadsRdd.

HtsjdkReadsTraversalParameters<T extends htsjdk.samtools.util.Locatable> - Class in org.disq_bio.disq

Holds parameters controlling which reads get returned when reading a HtsjdkReadsRdd.

HtsjdkReadsTraversalParameters(List<T>, boolean) - Constructor for class org.disq_bio.disq.HtsjdkReadsTraversalParameters

HtsjdkVariantsRdd - Class in org.disq_bio.disq

A HtsjdkVariantsRdd is the distributed equivalent of a htsjdk VCFFileReader.

HtsjdkVariantsRdd(VCFHeader, JavaRDD<VariantContext>) - Constructor for class org.disq_bio.disq.HtsjdkVariantsRdd

HtsjdkVariantsRddStorage - Class in org.disq_bio.disq

The entry point for reading or writing a HtsjdkVariantsRdd.

M

makeDefault(JavaSparkContext) - Static method in class org.disq_bio.disq.HtsjdkReadsRddStorage

Create a HtsjdkReadsRddStorage from a Spark context object.

makeDefault(JavaSparkContext) - Static method in class org.disq_bio.disq.HtsjdkVariantsRddStorage

Create a HtsjdkVariantsRddStorage from a Spark context object.

MULTIPLE - org.disq_bio.disq.FileCardinalityWriteOption

Write multiple files in a directory specified by the path.

O

org.disq_bio.disq - package org.disq_bio.disq

org.disq_bio.disq.serializer - package org.disq_bio.disq.serializer

R

read(String) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

Read reads from the given path.

read(String) - Method in class org.disq_bio.disq.HtsjdkVariantsRddStorage

Read variants from the given path.

read(String, List<T>) - Method in class org.disq_bio.disq.HtsjdkVariantsRddStorage

Read variants from the given path, using the given intervals to filter the variants.

read(String, HtsjdkReadsTraversalParameters<T>) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

Read reads from the given path, using the given traversal parameters to filter the reads.

ReadsFormatWriteOption - Enum in org.disq_bio.disq

An option for configuring which format to write a HtsjdkReadsRdd as.

referenceSourcePath(String) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

registerClasses(Kryo) - Method in class org.disq_bio.disq.serializer.DisqKryoRegistrator

registerDisqClasses(Kryo) - Static method in class org.disq_bio.disq.serializer.DisqKryoRegistrator

Register all classes serialized in Disq with the specified Kryo instance.

S

SAM - org.disq_bio.disq.ReadsFormatWriteOption

SAM format

sbiIndexGranularity(long) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

SbiWriteOption - Enum in org.disq_bio.disq

An option for for enabling or disabling writing SBI files.

SINGLE - org.disq_bio.disq.FileCardinalityWriteOption

Write a single file specified by the path.

splitSize(int) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

splitSize(int) - Method in class org.disq_bio.disq.HtsjdkVariantsRddStorage

T

TabixIndexWriteOption - Enum in org.disq_bio.disq

An option for for enabling or disabling writing tabix files.

TempPartsDirectoryWriteOption - Class in org.disq_bio.disq

An option for controlling which directory to write temporary part files to when writing output as a single file.

TempPartsDirectoryWriteOption(String) - Constructor for class org.disq_bio.disq.TempPartsDirectoryWriteOption

U

useNio(boolean) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

V

validationStringency(ValidationStringency) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

valueOf(String) - Static method in enum org.disq_bio.disq.BaiWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.CraiWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.FileCardinalityWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.ReadsFormatWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.SbiWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.TabixIndexWriteOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.disq_bio.disq.VariantsFormatWriteOption

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.disq_bio.disq.BaiWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.CraiWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.FileCardinalityWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.ReadsFormatWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.SbiWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.TabixIndexWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.disq_bio.disq.VariantsFormatWriteOption

Returns an array containing the constants of this enum type, in the order they are declared.

VariantsFormatWriteOption - Enum in org.disq_bio.disq

An option for configuring which format to write a HtsjdkVariantsRdd as.

VCF - org.disq_bio.disq.VariantsFormatWriteOption

VCF format

VCF_BGZ - org.disq_bio.disq.VariantsFormatWriteOption

block compressed VCF format (.vcf.bgz)

VCF_GZ - org.disq_bio.disq.VariantsFormatWriteOption

block compressed VCF format (.vcf.gz)

W

write(HtsjdkReadsRdd, String, WriteOption...) - Method in class org.disq_bio.disq.HtsjdkReadsRddStorage

Write reads to a file or files specified by the given path.

write(HtsjdkVariantsRdd, String, WriteOption...) - Method in class org.disq_bio.disq.HtsjdkVariantsRddStorage

Write variants to a file or files specified by the given path.

WriteOption - Interface in org.disq_bio.disq

An option for configuring how to write output.

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