org.bdgenomics.adam.api.java

# JavaADAMContext

#### class JavaADAMContext extends Serializable

The JavaADAMContext provides java-friendly functions on top of ADAMContext.

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### Instance Constructors

1. #### new JavaADAMContext(ac: ADAMContext)

   ac

     The ADAMContext to wrap.

### Value Members

1. #### final def !=(arg0: AnyRef): Boolean

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2. #### final def !=(arg0: Any): Boolean

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3. #### final def ##(): Int

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4. #### final def ==(arg0: AnyRef): Boolean

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5. #### final def ==(arg0: Any): Boolean

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6. #### val ac: ADAMContext

   The ADAMContext to wrap.

7. #### final def asInstanceOf[T0]: T0

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8. #### def clone(): AnyRef

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9. #### final def eq(arg0: AnyRef): Boolean

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10. #### def equals(arg0: Any): Boolean

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11. #### def finalize(): Unit

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12. #### final def getClass(): Class[_]

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13. #### def getSparkContext: JavaSparkContext

    returns

      Returns the Java Spark Context associated with this Java ADAM Context.

14. #### def hashCode(): Int

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15. #### final def isInstanceOf[T0]: Boolean

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16. #### 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

17. #### 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

18. #### 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

19. #### 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

20. #### 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

21. #### 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

22. #### 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

23. #### 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

24. #### 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

25. #### 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

26. #### 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

27. #### 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

28. #### 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

29. #### 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

30. #### 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

31. #### final def ne(arg0: AnyRef): Boolean

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32. #### final def notify(): Unit

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33. #### final def notifyAll(): Unit

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34. #### final def synchronized[T0](arg0: ⇒ T0): T0

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35. #### def toString(): String

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36. #### final def wait(): Unit

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