JavaADAMContext

Instance Constructors

new JavaADAMContext(ac: ADAMContext)

ac
The ADAMContext to wrap.

Value Members

final def !=(arg0: AnyRef): Boolean

Definition Classes
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final def !=(arg0: Any): Boolean

Definition Classes
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final def ##(): Int

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final def ==(arg0: AnyRef): Boolean

Definition Classes
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final def ==(arg0: Any): Boolean

Definition Classes
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val ac: ADAMContext

The ADAMContext to wrap.
final def asInstanceOf[T0]: T0

Definition Classes
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def clone(): AnyRef

Attributes
protected[java.lang]
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@throws( ... )
final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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def finalize(): Unit

Attributes
protected[java.lang]
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@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
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def getSparkContext: JavaSparkContext

returns
Returns the Java Spark Context associated with this Java ADAM Context.
def hashCode(): Int

Definition Classes
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final def isInstanceOf[T0]: Boolean

Definition Classes
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def loadAlignments(pathName: String, stringency: ValidationStringency): AlignmentRecordRDD

Load alignment records into an AlignmentRecordRDD (java-friendly method).
Load alignment records into an AlignmentRecordRDD (java-friendly method).
Loads path names ending in: * .bam/.cram/.sam as BAM/CRAM/SAM format, * .fa/.fasta as FASTA format, * .fq/.fastq as FASTQ format, and * .ifq as interleaved FASTQ format.
If none of these match, fall back to Parquet + Avro.
For FASTA, FASTQ, and interleaved FASTQ formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load alignment records from. Globs/directories are supported, although file extension must be present for BAM/CRAM/SAM, FASTA, and FASTQ formats.
stringency
The validation stringency to use when validating BAM/CRAM/SAM or FASTQ formats.
returns
Returns an AlignmentRecordRDD which wraps the RDD of alignment records, sequence dictionary representing contigs the alignment records may be aligned to, and the record group dictionary for the alignment records if one is available.

See also
ADAMContext#loadAlignments
def loadAlignments(pathName: String): AlignmentRecordRDD

Load alignment records into an AlignmentRecordRDD (java-friendly method).
Load alignment records into an AlignmentRecordRDD (java-friendly method).
Loads path names ending in: * .bam/.cram/.sam as BAM/CRAM/SAM format, * .fa/.fasta as FASTA format, * .fq/.fastq as FASTQ format, and * .ifq as interleaved FASTQ format.
If none of these match, fall back to Parquet + Avro.
For FASTA, FASTQ, and interleaved FASTQ formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load alignment records from. Globs/directories are supported, although file extension must be present for BAM/CRAM/SAM, FASTA, and FASTQ formats.
returns
Returns an AlignmentRecordRDD which wraps the RDD of alignment records, sequence dictionary representing contigs the alignment records may be aligned to, and the record group dictionary for the alignment records if one is available.

See also
ADAMContext#loadAlignments
def loadContigFragments(pathName: String): NucleotideContigFragmentRDD

Load nucleotide contig fragments into a NucleotideContigFragmentRDD (java-friendly method).
Load nucleotide contig fragments into a NucleotideContigFragmentRDD (java-friendly method).
If the path name has a .fa/.fasta extension, load as FASTA format. Else, fall back to Parquet + Avro.
For FASTA format, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load nucleotide contig fragments from. Globs/directories are supported, although file extension must be present for FASTA format.
returns
Returns a NucleotideContigFragmentRDD.

See also
ADAMContext#loadContigFragments
def loadCoverage(pathName: String, stringency: ValidationStringency): CoverageRDD

Load features into a FeatureRDD and convert to a CoverageRDD (java-friendly method).
Load features into a FeatureRDD and convert to a CoverageRDD (java-friendly method). Coverage is stored in the score field of Feature.
Loads path names ending in: * .bed as BED6/12 format, * .gff3 as GFF3 format, * .gtf/.gff as GTF/GFF2 format, * .narrow[pP]eak as NarrowPeak format, and * .interval_list as IntervalList format.
If none of these match, fall back to Parquet + Avro.
For BED6/12, GFF3, GTF/GFF2, NarrowPeak, and IntervalList formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load features from. Globs/directories are supported, although file extension must be present for BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
stringency
The validation stringency to use when validating BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
returns
Returns a FeatureRDD converted to a CoverageRDD.

See also
ADAMContext#loadCoverage
def loadCoverage(pathName: String): CoverageRDD

Load features into a FeatureRDD and convert to a CoverageRDD (java-friendly method).
Load features into a FeatureRDD and convert to a CoverageRDD (java-friendly method). Coverage is stored in the score field of Feature.
Loads path names ending in: * .bed as BED6/12 format, * .gff3 as GFF3 format, * .gtf/.gff as GTF/GFF2 format, * .narrow[pP]eak as NarrowPeak format, and * .interval_list as IntervalList format.
If none of these match, fall back to Parquet + Avro.
For BED6/12, GFF3, GTF/GFF2, NarrowPeak, and IntervalList formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load features from. Globs/directories are supported, although file extension must be present for BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
returns
Returns a FeatureRDD converted to a CoverageRDD.

See also
ADAMContext#loadCoverage
def loadFeatures(pathName: String, stringency: ValidationStringency): FeatureRDD

Load features into a FeatureRDD (java-friendly method).
Load features into a FeatureRDD (java-friendly method).
Loads path names ending in: * .bed as BED6/12 format, * .gff3 as GFF3 format, * .gtf/.gff as GTF/GFF2 format, * .narrow[pP]eak as NarrowPeak format, and * .interval_list as IntervalList format.
If none of these match, fall back to Parquet + Avro.
For BED6/12, GFF3, GTF/GFF2, NarrowPeak, and IntervalList formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load features from. Globs/directories are supported, although file extension must be present for BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
stringency
The validation stringency to use when validating BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
returns
Returns a FeatureRDD.

See also
ADAMContext#loadFeatures
def loadFeatures(pathName: String): FeatureRDD

Load features into a FeatureRDD (java-friendly method).
Load features into a FeatureRDD (java-friendly method).
Loads path names ending in: * .bed as BED6/12 format, * .gff3 as GFF3 format, * .gtf/.gff as GTF/GFF2 format, * .narrow[pP]eak as NarrowPeak format, and * .interval_list as IntervalList format.
If none of these match, fall back to Parquet + Avro.
For BED6/12, GFF3, GTF/GFF2, NarrowPeak, and IntervalList formats, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load features from. Globs/directories are supported, although file extension must be present for BED6/12, GFF3, GTF/GFF2, NarrowPeak, or IntervalList formats.
returns
Returns a FeatureRDD.

See also
ADAMContext#loadFeatures
def loadFragments(pathName: String, stringency: ValidationStringency): FragmentRDD

Load fragments into a FragmentRDD (java-friendly method).
Load fragments into a FragmentRDD (java-friendly method).
Loads path names ending in: * .bam/.cram/.sam as BAM/CRAM/SAM format and * .ifq as interleaved FASTQ format.
If none of these match, fall back to Parquet + Avro.
For interleaved FASTQ format, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load fragments from. Globs/directories are supported, although file extension must be present for BAM/CRAM/SAM and FASTQ formats.
stringency
The validation stringency to use when validating BAM/CRAM/SAM or FASTQ formats.
returns
Returns a FragmentRDD.

See also
ADAMContext#loadFragments
def loadFragments(pathName: String): FragmentRDD

Load fragments into a FragmentRDD (java-friendly method).
Load fragments into a FragmentRDD (java-friendly method).
Loads path names ending in: * .bam/.cram/.sam as BAM/CRAM/SAM format and * .ifq as interleaved FASTQ format.
If none of these match, fall back to Parquet + Avro.
For interleaved FASTQ format, compressed files are supported through compression codecs configured in Hadoop, which by default include .gz and .bz2, but can include more.
pathName
The path name to load fragments from. Globs/directories are supported, although file extension must be present for BAM/CRAM/SAM and FASTQ formats.
returns
Returns a FragmentRDD.

See also
ADAMContext#loadFragments
def loadGenotypes(pathName: String, stringency: ValidationStringency): GenotypeRDD

Load genotypes into a GenotypeRDD (java-friendly method).
Load genotypes into a GenotypeRDD (java-friendly method).
If the path name has a .vcf/.vcf.gz/.vcf.bgzf/.vcf.bgz extension, load as VCF format. Else, fall back to Parquet + Avro.
pathName
The path name to load genotypes from. Globs/directories are supported, although file extension must be present for VCF format.
stringency
The validation stringency to use when validating VCF format.
returns
Returns a GenotypeRDD.

See also
ADAMContext#loadGenotypes
def loadGenotypes(pathName: String): GenotypeRDD

Load genotypes into a GenotypeRDD (java-friendly method).
Load genotypes into a GenotypeRDD (java-friendly method).
If the path name has a .vcf/.vcf.gz/.vcf.bgzf/.vcf.bgz extension, load as VCF format. Else, fall back to Parquet + Avro.
pathName
The path name to load genotypes from. Globs/directories are supported, although file extension must be present for VCF format.
returns
Returns a GenotypeRDD.

See also
ADAMContext#loadGenotypes
def loadReferenceFile(pathName: String): ReferenceFile

Load reference sequences into a broadcastable ReferenceFile (java-friendly method).
Load reference sequences into a broadcastable ReferenceFile (java-friendly method).
If the path name has a .2bit extension, loads a 2bit file. Else, uses loadContigFragments to load the reference as an RDD, which is then collected to the driver. Uses a maximum fragment length of 10kbp.
pathName
The path name to load reference sequences from. Globs/directories for 2bit format are not supported.
returns
Returns a broadcastable ReferenceFile.

See also
loadContigFragments
def loadReferenceFile(pathName: String, maximumLength: Long): ReferenceFile

Load reference sequences into a broadcastable ReferenceFile (java-friendly method).
Load reference sequences into a broadcastable ReferenceFile (java-friendly method).
If the path name has a .2bit extension, loads a 2bit file. Else, uses loadContigFragments to load the reference as an RDD, which is then collected to the driver.
pathName
The path name to load reference sequences from. Globs/directories for 2bit format are not supported.
maximumLength
Maximum fragment length. Defaults to 10000L. Values greater than 1e9 should be avoided.
returns
Returns a broadcastable ReferenceFile.

See also
loadContigFragments
def loadVariants(pathName: String, stringency: ValidationStringency): VariantRDD

Load variants into a VariantRDD (java-friendly method).
Load variants into a VariantRDD (java-friendly method).
If the path name has a .vcf/.vcf.gz/.vcf.bgzf/.vcf.bgz extension, load as VCF format. Else, fall back to Parquet + Avro.
pathName
The path name to load variants from. Globs/directories are supported, although file extension must be present for VCF format.
stringency
The validation stringency to use when validating VCF format.
returns
Returns a VariantRDD.

See also
ADAMContext#loadVariants
def loadVariants(pathName: String): VariantRDD

Load variants into a VariantRDD (java-friendly method).
Load variants into a VariantRDD (java-friendly method).
If the path name has a .vcf/.vcf.gz/.vcf.bgzf/.vcf.bgz extension, load as VCF format. Else, fall back to Parquet + Avro.
pathName
The path name to load variants from. Globs/directories are supported, although file extension must be present for VCF format.
returns
Returns a VariantRDD.

See also
ADAMContext#loadVariants
final def ne(arg0: AnyRef): Boolean

Definition Classes
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final def notify(): Unit

Definition Classes
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final def notifyAll(): Unit

Definition Classes
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final def synchronized[T0](arg0: ⇒ T0): T0

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def toString(): String

Definition Classes
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final def wait(): Unit

Definition Classes
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Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
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@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
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@throws( ... )

class JavaADAMContext extends Serializable

Instance Constructors

new JavaADAMContext(ac: ADAMContext)

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

val ac: ADAMContext

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def getSparkContext: JavaSparkContext

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def loadAlignments(pathName: String, stringency: ValidationStringency): AlignmentRecordRDD

def loadAlignments(pathName: String): AlignmentRecordRDD

def loadContigFragments(pathName: String): NucleotideContigFragmentRDD

def loadCoverage(pathName: String, stringency: ValidationStringency): CoverageRDD

def loadCoverage(pathName: String): CoverageRDD

def loadFeatures(pathName: String, stringency: ValidationStringency): FeatureRDD

def loadFeatures(pathName: String): FeatureRDD

def loadFragments(pathName: String, stringency: ValidationStringency): FragmentRDD

def loadFragments(pathName: String): FragmentRDD

def loadGenotypes(pathName: String, stringency: ValidationStringency): GenotypeRDD

def loadGenotypes(pathName: String): GenotypeRDD

def loadReferenceFile(pathName: String): ReferenceFile

def loadReferenceFile(pathName: String, maximumLength: Long): ReferenceFile

def loadVariants(pathName: String, stringency: ValidationStringency): VariantRDD

def loadVariants(pathName: String): VariantRDD

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped