class JavaADAMContext extends Serializable
The JavaADAMContext provides java-friendly functions on top of ADAMContext.
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JavaADAMContext(ac: ADAMContext)
- ac
The ADAMContext to wrap.
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- val ac: ADAMContext
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def
getSparkContext: JavaSparkContext
- returns
Returns the Java Spark Context associated with this Java ADAM Context.
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def
loadAlignments(pathName: String, stringency: ValidationStringency): AlignmentRecordDataset
(Java-specific) Load alignment records into an AlignmentRecordDataset.
(Java-specific) Load alignment records into an AlignmentRecordDataset.
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 AlignmentRecordDataset which wraps the genomic dataset of alignment records, sequence dictionary representing contigs the alignment records may be aligned to, and the read group dictionary for the alignment records if one is available.
- See also
ADAMContext#loadAlignments
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def
loadAlignments(pathName: String): AlignmentRecordDataset
(Java-specific) Load alignment records into an AlignmentRecordDataset.
(Java-specific) Load alignment records into an AlignmentRecordDataset.
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 AlignmentRecordDataset which wraps the genomic dataset of alignment records, sequence dictionary representing contigs the alignment records may be aligned to, and the read group dictionary for the alignment records if one is available.
- See also
ADAMContext#loadAlignments
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def
loadContigFragments(pathName: String): NucleotideContigFragmentDataset
(Java-specific) Load nucleotide contig fragments into a NucleotideContigFragmentDataset.
(Java-specific) Load nucleotide contig fragments into a NucleotideContigFragmentDataset.
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 NucleotideContigFragmentDataset.
- See also
ADAMContext#loadContigFragments
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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
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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
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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
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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
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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
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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
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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
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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
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def
loadIndexedBam(pathName: String, viewRegions: List[ReferenceRegion], stringency: ValidationStringency): AlignmentRecordDataset
(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 alignment records 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 AlignmentRecordDataset which wraps the genomic dataset of alignment records, sequence dictionary representing contigs the alignment records may be aligned to, and the read group dictionary for the alignment records if one is available.
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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 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
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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 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
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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
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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
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