VCFHeaderUtils

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1. final def !=(arg0: Any): Boolean

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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4. val INFER_HEADER: String

   

5. val VCF_HEADER_KEY: String

   

6. final def asInstanceOf[T0]: T0

   

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7. def clone(): AnyRef

   

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8. def createHeaderRDD(spark: SparkSession, files: Seq[String]): RDD[VCFHeader]

   

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 getUniqueHeaderLines(headers: RDD[VCFHeader], getNonSchemaHeaderLines: Boolean): Seq[VCFHeaderLine]

    

    Find the unique desired header lines from an RDD of VCF headers.

    Find the unique desired header lines from an RDD of VCF headers. If lines of the same class found with the same ID, we pick one unless they are incompatible. If there are incompatible lines, IllegalArgumentException is thrown. Incompatible lines are: - FORMAT or INFO lines with the same ID but different types or counts - contig lines with the same ID but different lengths

    headers

    VCF headers to parse header lines from

    getNonSchemaHeaderLines

    If false, parses only INFO and FORMAT lines. If true, also parses contig and filter lines.

14. def hashCode(): Int

    

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15. final def isInstanceOf[T0]: Boolean

    

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16. lazy val logger: Logger

    

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

    

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18. final def notify(): Unit

    

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19. final def notifyAll(): Unit

    

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20. def parseHeaderFromString(s: String): VCFHeader

    

21. def readHeaderLines(spark: SparkSession, files: Seq[String], getNonSchemaHeaderLines: Boolean): Seq[VCFHeaderLine]

    

    A convenience function to parse the headers from a set of VCF files and return the desired header lines.

    A convenience function to parse the headers from a set of VCF files and return the desired header lines.

    files

    VCF files to parse header lines from

    getNonSchemaHeaderLines

    If false, parses only INFO and FORMAT lines. If true, also parses contig and filter lines.

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

    

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23. def toString(): String

    

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24. final def wait(): Unit

    

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

    

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

    

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