class JavaADAMContext extends Serializable
The JavaADAMContext provides java-friendly functions on top of ADAMContext.
- Alphabetic
- By Inheritance
- JavaADAMContext
- Serializable
- Serializable
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
-
new
JavaADAMContext(ac: ADAMContext)
- ac
The ADAMContext to wrap.
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val ac: ADAMContext
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
getSparkContext: JavaSparkContext
- returns
Returns the Java Spark Context associated with this Java ADAM Context.
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
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#loadFastaDna
ADAMContext#loadParquetSequences
-
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#loadFastaProtein
ADAMContext#loadParquetSequences
-
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#loadFastaRna
ADAMContext#loadParquetSequences
-
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
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
- Deprecated
(Since version ) see corresponding Javadoc for more information.