SampleCompare

Value Members

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

   

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2. final def ##(): Int

   

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3. def +=(other: SampleCompare): SampleCompare

   

   This will combine 2 SampleCompare classes together

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

   

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5. def addRecord(record: VariantContext, sampleToSampleMinDepth: Option[Int]): Unit

   

   Checking a record to add to compate matrix

   Checking a record to add to compate matrix

   record

   VariantContext to add

   sampleToSampleMinDepth

   If set a genotype need DP to be >=. This does depend on the DP fiald in the vcf record

6. def allelesCount(id1: Int)(id2: Int): Long

   

   Return the number of overlapping alleles

7. def allelesCount(name1: String)(name2: String): Long

   

   Return the number of overlapping alleles

8. val allelesCounts: Array[Array[Long]]

   

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9. final def asInstanceOf[T0]: T0

   

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10. def clone(): AnyRef

    

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    protected[java.lang]

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    @throws( ... )

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

    

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12. def equals(arg0: Any): Boolean

    

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13. def finalize(): Unit

    

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    @throws( classOf[java.lang.Throwable] )

14. def genotypesCount(id1: Int)(id2: Int): Long

    

    Return the number of overlapping genotypes

15. def genotypesCount(name1: String)(name2: String): Long

    

    Return the number of overlapping genotypes

16. val genotypesCounts: Array[Array[Long]]

    

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    protected

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

    

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18. def hashCode(): Int

    

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19. final def isInstanceOf[T0]: Boolean

    

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

    

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21. final def notify(): Unit

    

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22. final def notifyAll(): Unit

    

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23. val samples: Map[String, Int]

    

    This map binds names to sample index

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

    

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25. def toString(): String

    

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26. final def wait(): Unit

    

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    @throws( ... )

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

    

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    @throws( ... )

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

    

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29. def writeAllFiles(outputDir: File): Unit

    

    Write all posible files to directory

    Write all posible files to directory

    outputDir

    Directory to write to

30. def writeAlleleOverlap(outputFile: File, relative: Boolean = false): Unit

    

    Writer allele matrix to a file

    Writer allele matrix to a file

    outputFile

    File to write to

    relative

    If true values will be devided by the total number of counts for a sample

31. def writeGenotypeOverlap(outputFile: File, relative: Boolean = false): Unit

    

    Writes genotype matrix to a file

    Writes genotype matrix to a file

    outputFile

    File to write to

    relative

    If true values will be devided by the total number of counts for a sample

32. def writeOverlapFile(counts: Array[Array[Long]], outputFile: File, relative: Boolean = false): Unit

    

    Writing a matrix to a file

    Writing a matrix to a file

    counts

    Matrix to write

    outputFile

    File to write to

    relative

    If true values will be devided by the total number of counts for a sample

    Attributes

    protected