bgen

Type Members

1. class BgenFileFormat extends FileFormat with DataSourceRegister with Serializable with GlowLogging

   

2. class BgenRecordWriter extends GlowLogging

   

   Writes BGEN records.

3. class BgenRowToInternalRowConverter extends GlowLogging

   

   Converts BgenRows into InternalRow with a given required schema.

   Converts BgenRows into InternalRow with a given required schema. During construction, this class will throw an IllegalArgumentException if any of the fields in the required schema cannot be derived from a BGEN record.

4. class BigBgenDatasource extends BigFileDatasource with DataSourceRegister

   

5. case class BigBgenOptions(bitsPerProb: Int, maxPloidy: Int, defaultPloidy: Int, defaultPhasing: Boolean) extends Product with Serializable

   

6. class ComDatabricksBgenFileFormat extends BgenFileFormat with ComDatabricksDataSource

   

7. class ComDatabricksBigBgenDatasource extends BigBgenDatasource with ComDatabricksDataSource

   

8. case class FractionalPartIndex(fractionalPart: Double, index: Int) extends Product with Serializable

   

9. case class GenotypeCharacteristics(numAlleles: Int, phased: Boolean, ploidy: Int) extends Product with Serializable

   

10. class InternalRowToBgenRowConverter extends GlowLogging

    

    Converts internal rows to BGEN rows.

    Converts internal rows to BGEN rows. Includes logic to infer phasing and ploidy if missing (eg. when converting from VCF rows with no GT field), using the number of alleles and the number of posterior probabilities.

    - If phasing and ploidy are missing, we assume ploidy is defaultPloidy. - If phasing is missing:

    • If no posterior probabilities are present, we assume phasing is defaultPhasing.
    • If the number of posterior probabilities matches the case that the probability represents:
      • Either phased or unphased data: we assume phasing is defaultPhasing.
      • Phased data: we assume the data is phased.
      • Unphased data: we assume the data is unphased.
      • Neither: we throw an exception - If ploidy is missing:
    • If no posterior probabilities are present, we assume ploidy is defaultPloidy.
    • If phased, we try to calculate the ploidy directly.
    • If unphased, we try to find the ploidy between [1, maxPloidy].

    Exceptions thrown

    IllegalStateException if phasing or ploidy cannot be inferred or a single row contains both unphased and phased data.

11. case class ProbabilityBlockSize(probabilitiesPerBlock: Int, numBlocks: Int) extends Product with Serializable

    

12. sealed trait SNPBlockCompression extends AnyRef

    

13. class SortByDescendingFractionalPart extends Comparator[FractionalPartIndex]