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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 INDEX_SUFFIX: String
5.  final def asInstanceOf[T0]: T0

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6.  def clone(): AnyRef

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7.  def createVCFCodec(path: String, conf: Configuration): (VCFHeader, VCFCodec)

   Reads the header of a VCF file to generate an object representing the information in the header and a derived VCFCodec that can parse the rest of the file.

   Reads the header of a VCF file to generate an object representing the information in the header and a derived VCFCodec that can parse the rest of the file.

   The logic to parse the header is adapted from org.seqdoop.hadoop_bam.VCFRecordReader.

8.  final def eq(arg0: AnyRef): Boolean

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9.  def equals(arg0: Any): Boolean

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10.  def finalize(): Unit

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11.  final def getClass(): Class[_]

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12.  def hadoopConfWithBGZ(conf: Configuration): Configuration

    Adds BGZF support to an existing Hadoop conf.

13.  def hashCode(): Int

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14.  val idxLock: Striped[Lock]
15.  def isGzip(split: PartitionedFile, conf: Configuration): Boolean

    Checks whether a file is gzipped (not block gzipped).

16.  final def isInstanceOf[T0]: Boolean

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17.  def isValidBGZ(path: Path, conf: Configuration): Boolean

    Checks whether the file is a valid bgzipped file Used by filteredVariantBlockRange to abandon use of tabix if the file is not bgzipped.

18.  final def ne(arg0: AnyRef): Boolean

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19.  final def notify(): Unit

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20.  final def notifyAll(): Unit

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

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22.  def toString(): String

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23.  final def wait(): Unit

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

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25.  final def wait(arg0: Long): Unit

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