org.anduril.runtime.table

Table

object Table

Convenience object for creating table readers and writers, and containing various constants.

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  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 ColumnFASTQ: Seq[String]

    Names of the columns in FASTQ tables.

  7. val ColumnsBED6: Seq[String]

    Names of the first six columns for BED.

  8. val ColumnsFASTA: Seq[String]

    Names of the columns in FASTA tables.

  9. val ColumnsVCF: Seq[String]

    Standard names of the first eight columns for VCF.

  10. val FormatAuto: String

    Constant for the automatic file format, in which format is inferred from file name.

  11. val FormatBED: String

    Constant for the BED file format.

  12. val FormatCSV: String

    Constant for tab-separated file format.

  13. val FormatFASTA: String

    Constant for the FASTA file format.

  14. val FormatFASTQ: String

    Constant for the FASTQ file format.

  15. val FormatVCF: String

    Constant for variant call format (VCF).

  16. final def asInstanceOf[T0]: T0

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  17. def clone(): AnyRef

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  18. final def eq(arg0: AnyRef): Boolean

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  20. def finalize(): Unit

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  21. final def getClass(): Class[_]

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  22. def hashCode(): Int

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  23. final def isInstanceOf[T0]: Boolean

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  24. final def ne(arg0: AnyRef): Boolean

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  25. final def notify(): Unit

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  26. final def notifyAll(): Unit

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  27. def openGZFileReader(file: File): LineNumberReader

    Open an optionally gzipped text file for reading.

    Open an optionally gzipped text file for reading. File format (uncompressed or gzipped) is detected automatically.

    file

    Uncompressed or gzipped file.

  28. def reader(source: File, format: String = FormatAuto): Table

    Create a table reader from a file.

    Create a table reader from a file. Optionally, the file may be gzipped.

    source

    Table file

    format

    Format of the table file, as one of the FormatX constants. If FormatAuto is given, the format is inferred from the file name.

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

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  30. def toString(): String

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  31. final def wait(): Unit

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

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  33. final def wait(arg0: Long): Unit

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  34. def writer(template: Table, target: File, format: String): TableWriter

    Create a table writer based on a template table that defines output columns.

    Create a table writer based on a template table that defines output columns.

    template

    Template table from which columns are taken.

    target

    File for writing the table.

    format

    Format of the output table, as one of the FormatX constants. If FormatAuto is given, the format is inferred from the file name.

  35. def writer(template: Table, target: OutputStream, format: String): TableWriter

    Create a table writer based on a template table that defines output columns.

    Create a table writer based on a template table that defines output columns.

    template

    Template table from which columns are taken.

    target

    Stream for writing the table.

    format

    Format of the output table, as one of the FormatX constants. FormatAuto is not supported in this variant.

  36. def writer(columns: Seq[String], target: File, format: String = FormatAuto): TableWriter

    Create a table writer based on a list of column names.

    Create a table writer based on a list of column names.

    columns

    Column names for the output table.

    target

    File for writing the table.

    format

    Format of the output table, as one of the FormatX constants. If FormatAuto is given, the format is inferred from the file name.

  37. def writer(columns: Seq[String], target: OutputStream, format: String): TableWriter

    Create a table writer based on a list of column names.

    Create a table writer based on a list of column names.

    columns

    Column names for the output table.

    target

    Stream for writing the table.

    format

    Format of the output table, as one of the FormatX constants. FormatAuto is not supported in this variant.

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