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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.  final def asInstanceOf[T0]: T0

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5.  val changedFieldName: String
6.  def clone(): AnyRef

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

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8.  def equals(arg0: Any): Boolean

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9.  val errorMessageFieldName: String
10.  def finalize(): Unit

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11.  final def getClass(): Class[_]

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12.  def hashCode(): Int

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13.  final def isInstanceOf[T0]: Boolean

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14.  def isSNP(refAllele: String, altAlleles: Array[String]): Boolean
15.  def isSymbolic(altAlleles: Array[String]): Boolean
16.  lazy val logger: Logger

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

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18.  val normalizationResultFieldName: String
19.  val normalizationResultStructType: StructType
20.  val normalizationStatusFieldName: String
21.  val normalizationStatusStructField: StructField
22.  def normalizeVariant(contigName: String, start: Long, end: Long, refAllele: String, altAlleles: Array[String], refGenomeIndexedFasta: IndexedFastaSequenceFile): InternalRow

    Contains the main normalization logic.

    Contains the main normalization logic. Given contigName, start, end, refAllele, and altAlleles of a variant as well as the indexed fasta file of the reference genome, creates an InternalRow of the normalization result.

    The algorithm has a logic similar to bcftools norm or vt normalize:

    It starts from the rightmost base of all alleles and scans one base at a time incrementing trimSize and nTrimmedBasesBeforeNextPadding as long as the bases of all alleles at that position are the same. If the beginning of any of the alleles is reached, all alleles are padded on the left by PAD_WINDOW_SIZE bases by reading from the reference genome and nTrimmedBaseBeforeNextPadding is reset. The process continues until a position is reached where all alleles do not have the same base or the beginning of the contig is reached. Next trimming from left starts and all bases common among all alleles from left are trimmed. Start and end are adjusted accordingly during the process.

    contigName

    : Contig name of the alleles

    start

    : 0-based start of the REF allele in an open-left closed-right interval system

    end

    : 0-based end of the REF allele in an open-left closed-right interval system

    refAllele

    : String containing refrence allele

    altAlleles

    : String array of alternate alleles

    refGenomeIndexedFasta

    : an IndexedFastaSequenceFile of the reference genome.

    returns

    normalization result as an InternalRow

23.  final def notify(): Unit

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24.  final def notifyAll(): Unit

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

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26.  def toString(): String

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27.  final def wait(): Unit

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

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

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