JavaADAMContext

Instance Constructors

new JavaADAMContext(ac: ADAMContext)

ac
The ADAMContext to wrap.

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
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final def ##(): Int

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
Any
def clone(): AnyRef

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

Definition Classes
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def equals(arg0: Any): Boolean

Definition Classes
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def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
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Annotations
@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
AnyRef → Any
final def isInstanceOf[T0]: Boolean

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

(Java-specific) Load alignments into an AlignmentDataset.
(Java-specific) Load alignments into an AlignmentDataset.
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 alignments 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 AlignmentDataset which wraps the genomic dataset of alignments, sequence dictionary representing contigs the alignments may be aligned to, and the read group dictionary for the alignments if one is available.

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

(Java-specific) Load alignments into an AlignmentDataset.
(Java-specific) Load alignments into an AlignmentDataset.
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 alignments from. Globs/directories are supported, although file extension must be present for BAM/CRAM/SAM, FASTA, and FASTQ formats.
returns
Returns an AlignmentDataset which wraps the genomic dataset of alignments, sequence dictionary representing contigs the alignments may be aligned to, and the read group dictionary for the alignments if one is available.

See also
ADAMContext#loadAlignments
def loadCoverage(pathName: String, stringency: ValidationStringency): CoverageDataset

(Java-specific) Load features into a FeatureDataset and convert to a CoverageDataset.
(Java-specific) Load features into a FeatureDataset and convert to a CoverageDataset. 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 FeatureDataset converted to a CoverageDataset.

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

(Java-specific) Load features into a FeatureDataset and convert to a CoverageDataset.
(Java-specific) Load features into a FeatureDataset and convert to a CoverageDataset. 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 FeatureDataset converted to a CoverageDataset.

See also
ADAMContext#loadCoverage
def loadDnaSequences(pathName: String): SequenceDataset

(Java-specific) Load DNA sequences into a SequenceDataset.
(Java-specific) Load DNA sequences into a SequenceDataset.
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 sequences from. Globs/directories are supported, although file extension must be present for FASTA format.
returns
Returns a SequenceDataset containing DNA sequences.

See also
ADAMContext#loadParquetSequences
ADAMContext#loadFastaDna
def loadFeatures(pathName: String, stringency: ValidationStringency): FeatureDataset

(Java-specific) Load features into a FeatureDataset.
(Java-specific) Load features into a FeatureDataset.
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 FeatureDataset.

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

(Java-specific) Load features into a FeatureDataset.
(Java-specific) Load features into a FeatureDataset.
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 FeatureDataset.

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

(Java-specific) Load fragments into a FragmentDataset.
(Java-specific) Load fragments into a FragmentDataset.
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 FragmentDataset.

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

(Java-specific) Load fragments into a FragmentDataset.
(Java-specific) Load fragments into a FragmentDataset.
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 FragmentDataset.

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

(Java-specific) Load genotypes into a GenotypeDataset.
(Java-specific) Load genotypes into a GenotypeDataset.
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 GenotypeDataset.

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

(Java-specific) Load genotypes into a GenotypeDataset.
(Java-specific) Load genotypes into a GenotypeDataset.
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 GenotypeDataset.

See also
ADAMContext#loadGenotypes
def loadIndexedBam(pathName: String, viewRegions: List[ReferenceRegion], stringency: ValidationStringency): AlignmentDataset

(Java-specific) Functions like loadBam, but uses BAM index files to look at fewer blocks, and only returns records within the specified ReferenceRegions.
(Java-specific) Functions like loadBam, but uses BAM index files to look at fewer blocks, and only returns records within the specified ReferenceRegions. BAM index file required.
pathName
The path name to load indexed BAM formatted alignments from. Globs/directories are supported.
viewRegions
Iterable of ReferenceRegion we are filtering on.
stringency
The validation stringency to use when validating the BAM/CRAM/SAM format header. Defaults to ValidationStringency.STRICT.
returns
Returns an AlignmentDataset which wraps the genomic dataset of alignments, sequence dictionary representing contigs the alignments may be aligned to, and the read group dictionary for the alignments if one is available.
def loadProteinSequences(pathName: String): SequenceDataset

(Java-specific) Load protein sequences into a SequenceDataset.
(Java-specific) Load protein sequences into a SequenceDataset.
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 sequences from. Globs/directories are supported, although file extension must be present for FASTA format.
returns
Returns a SequenceDataset containing protein sequences.

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

(Java-specific) Load reference sequences into a broadcastable ReferenceFile.
(Java-specific) Load reference sequences into a broadcastable ReferenceFile.
If the path name has a .2bit extension, loads a 2bit file. Else, uses loadSlices 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
ADAMContext#loadSlices
def loadReferenceFile(pathName: String, maximumLength: Long): ReferenceFile

(Java-specific) Load reference sequences into a broadcastable ReferenceFile.
(Java-specific) Load reference sequences into a broadcastable ReferenceFile.
If the path name has a .2bit extension, loads a 2bit file. Else, uses loadSlices 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
ADAMContext#loadSlices
def loadRnaSequences(pathName: String): SequenceDataset

(Java-specific) Load RNA sequences into a SequenceDataset.
(Java-specific) Load RNA sequences into a SequenceDataset.
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 sequences from. Globs/directories are supported, although file extension must be present for FASTA format.
returns
Returns a SequenceDataset containing RNA sequences.

See also
ADAMContext#loadParquetSequences
ADAMContext#loadFastaRna
def loadSlices(pathName: String, maximumLength: Double): SliceDataset

(R-specific) Load slices into a SliceDataset.
(R-specific) Load slices into a SliceDataset.
If the path name has a .fa/.fasta extension, load as DNA in 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 DNA slices from. Globs/directories are supported, although file extension must be present for FASTA format.
maximumLength
Maximum fragment length, in Double data type to support dispatch from SparkR.
returns
Returns a SliceDataset.
def loadSlices(pathName: String, maximumLength: Integer): SliceDataset

(Java/Python-specific) Load slices into a SliceDataset.
(Java/Python-specific) Load slices into a SliceDataset.
If the path name has a .fa/.fasta extension, load as DNA in 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 DNA slices from. Globs/directories are supported, although file extension must be present for FASTA format.
maximumLength
Maximum slice length, reduced to Integer data type to support dispatch from Python.
returns
Returns a SliceDataset.
def loadVariants(pathName: String, stringency: ValidationStringency): VariantDataset

(Java-specific) Load variants into a VariantDataset.
(Java-specific) Load variants into a VariantDataset.
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 VariantDataset.

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

(Java-specific) Load variants into a VariantDataset.
(Java-specific) Load variants into a VariantDataset.
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 VariantDataset.

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

Definition Classes
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final def notify(): Unit

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final def notifyAll(): Unit

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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

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

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final def wait(arg0: Long): Unit

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Related Docs: object JavaADAMContext | package java

class JavaADAMContext extends Serializable

Instance Constructors

new JavaADAMContext(ac: ADAMContext)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

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): AlignmentDataset

def loadAlignments(pathName: String): AlignmentDataset

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

def loadCoverage(pathName: String): CoverageDataset

def loadDnaSequences(pathName: String): SequenceDataset

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

def loadFeatures(pathName: String): FeatureDataset

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

def loadFragments(pathName: String): FragmentDataset

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

def loadGenotypes(pathName: String): GenotypeDataset

def loadIndexedBam(pathName: String, viewRegions: List[ReferenceRegion], stringency: ValidationStringency): AlignmentDataset

def loadProteinSequences(pathName: String): SequenceDataset

def loadReferenceFile(pathName: String): ReferenceFile

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

def loadRnaSequences(pathName: String): SequenceDataset

def loadSlices(pathName: String, maximumLength: Double): SliceDataset

def loadSlices(pathName: String, maximumLength: Integer): SliceDataset

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

def loadVariants(pathName: String): VariantDataset

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

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