Index (Disq 0.3.3 API)

B C D F G H M O R S T U V W

B

BaiWriteOption - Enum in org.disq_bio.disq: An option for for enabling or disabling writing BAI files.

C

CraiWriteOption - Enum in org.disq_bio.disq: An option for for enabling or disabling writing CRAI files.

D

DisqKryoRegistrator - Class in org.disq_bio.disq.serializer: Kryo registrator for Disq.
DisqKryoRegistrator() - Constructor for class org.disq_bio.disq.serializer.DisqKryoRegistrator

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.

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, 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.
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.
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

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.
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.

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.

B C D F G H M O R S T U V W