VcfFilter

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

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

   

   Definition Classes

   AnyRef → Any

4. def aboutText: String

   

   Definition Classes

   ToolCommand

5. def advancedGroupFilter(record: VariantContext, groups: List[List[String]]): Boolean

   

   returns true when for all groups all or none members have a variants, records with partial groups are discarded

6. def allSamplesVariant(record: VariantContext): Boolean

   

   Checks if all samples are a variant

7. def argsParser: ArgsParser

   

   Definition Classes

   VcfFilter → ToolCommand

8. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

9. def calledIn(record: VariantContext, samples: List[String]): Boolean

   

   Checks if given samples are called

   Checks if given samples are called

   record

   VCF record

   samples

   Samples that need this sample to be called

   returns

   false when filters fail

10. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

11. def cmdArrayToArgs(args: Array[String]): Args

    

    Definition Classes

    ToolCommand

12. def contactText: String

    

    Definition Classes

    ToolCommand

13. def contributingText: String

    

    Definition Classes

    ToolCommand

14. def denovoTrio(record: VariantContext, trios: List[Trio], onlyLossHet: Boolean = false): Boolean

    

    Returns true when child got a deNovo variant

15. def descriptionText: String

    

    Definition Classes

    VcfFilter → ToolCommand

16. def documentationText: String

    

    Definition Classes

    ToolCommand

17. def emptyArgs: Args

    

    Definition Classes

    VcfFilter → ToolCommand

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

    

    Definition Classes

    AnyRef

19. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

20. def example(args: String*): String

    

    Definition Classes

    ToolCommand

21. def exampleText: String

    

    Definition Classes

    VcfFilter → ToolCommand

22. def filterHetVarToHomVar(record: VariantContext, sample1: String, sample2: String): Boolean

    

    Checks if sample1 is hetrozygous and if sample2 is homozygous for a alternative allele in sample1

23. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

24. def generateDocumentation(outputDirectory: File, version: String, release: Boolean): Unit

    

    Definition Classes

    ToolCommand

25. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

27. def hasCalls(record: VariantContext): Boolean

    

    returns true when record has calls

28. def hasGenotype(record: VariantContext, samplesGenotypes: List[(String, GenotypeType)]): Boolean

    

    Checks if given genotypes for given samples are there

    Checks if given genotypes for given samples are there

    record

    VCF record

    samplesGenotypes

    samples and their associated genotypes to be checked (of format sample:genotype)

    returns

    false when filter fails

29. def hasMinSampleDepth(record: VariantContext, minSampleDepth: Int, minSamplesPass: Int = 1): Boolean

    

    Checks if DP genotype field have a minimal value

    Checks if DP genotype field have a minimal value

    record

    VCF record

    minSampleDepth

    minimal depth

    minSamplesPass

    Minimal number of samples to pass filter

    returns

    true if filter passed

30. def hasMinTotalDepth(record: VariantContext, minTotalDepth: Int): Boolean

    

    returns true when DP INFO field is atleast the given value

31. def hasNonRefCalls(record: VariantContext): Boolean

    

    returns true record contains Non reference genotypes

32. def hasUniqeSample(record: VariantContext): Boolean

    

    Checks if there is a variant in only 1 sample

33. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

34. def inIdSet(record: VariantContext, idSet: Set[String]): Boolean

    

    Returns true when VCF record contains a ID from the given list

35. def infoFieldMustMatch(record: VariantContext, key: String, regex: Regex): Boolean

    

    A info field should match the given regex

36. def installationText: String

    

    Definition Classes

    ToolCommand

37. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

38. def logger: Logger

    

    Definition Classes

    Logging

39. def main(args: Array[String]): Unit

    

    Definition Classes

    VcfFilter → ToolCommand

40. def mainPageContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

41. def manualText: String

    

    Definition Classes

    VcfFilter → ToolCommand

42. def minAlternateDepth(record: VariantContext, minAlternateDepth: Int, minSamplesPass: Int = 1): Boolean

    

    Checks if non-ref AD genotype field have a minimal value

    Checks if non-ref AD genotype field have a minimal value

    record

    VCF record

    minAlternateDepth

    minimal depth

    minSamplesPass

    Minimal number of samples to pass filter

    returns

    true if filter passed

43. def minAvgVariantGq(record: VariantContext, minGQ: Option[Int]): Boolean

    

    This filters on the average GQ on all variants

    This filters on the average GQ on all variants

    record

    VCF record

    minGQ

    Minimal average GQ on variants

44. def minCalled(record: VariantContext, threshold: Int): Boolean

    

45. def minGenomeQuality(record: VariantContext, minGQ: Int, minSamplesPass: Int = 1): Boolean

    

    Checks if genome quality field has minimum value

    Checks if genome quality field has minimum value

    record

    VCF record

    minGQ

    smallest GQ allowed

    minSamplesPass

    number of samples to consider

46. def minQualscore(record: VariantContext, minQualScore: Double): Boolean

    

    Checks if record has atleast minQualScore

    Checks if record has atleast minQualScore

    record

    VCF record

    minQualScore

    Minimal quality score

    returns

    false when filters fail

47. def mustHaveVariant(record: VariantContext, samples: List[String]): Boolean

    

    Checks if given samples does have a variant hin this record

    Checks if given samples does have a variant hin this record

    record

    VCF record

    samples

    List of samples that should have this variant

    returns

    true if filter passed

48. def mustNotHaveVariant(record: VariantContext, samples: List[String]): Boolean

    

    Checks if given samples does have a variant hin this record

    Checks if given samples does have a variant hin this record

    record

    VCF record

    samples

    List of samples that should have this variant

    returns

    true if filter passed

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

    

    Definition Classes

    AnyRef

50. def notSameGenotype(record: VariantContext, sample1: String, sample2: String): Boolean

    

    Checks if given samples have the same genotype

51. final def notify(): Unit

    

    Definition Classes

    AnyRef

52. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

53. def readmeContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

54. def resToDom(record: VariantContext, trios: List[Trio]): Boolean

    

    Return true when variant is homozygous in the child and hetrozygous in parants

55. def sparkExample(args: String*): String

    

    Definition Classes

    ToolCommand

56. def sparkUnsafeExample(args: String*): String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef

58. def toString(): String

    

    Definition Classes

    AnyRef → Any

59. def toolName: String

    

    Definition Classes

    ToolCommand

60. def trioCompound(record: VariantContext, trios: List[Trio]): Boolean

    

    Returns true when variant a compound variant in the child and hetrozygous in parants

61. def uniqueVariantInSample(record: VariantContext, sample: String): Boolean

    

    Checks if given sample have alternative alleles that are unique in the VCF record

62. def unsafeExample(args: String*): String

    

    Definition Classes

    ToolCommand

63. def urlToolName: String

    

    Definition Classes

    ToolCommand

64. def usageHeaders: List[String]

    

    Attributes

    protected

    Definition Classes

    ToolCommand

65. def usageHtmlTable: String

    

    Definition Classes

    ToolCommand

66. def usageRows(parser: OptionParser[Args]): List[List[String]]

    

    Attributes

    protected

    Definition Classes

    ToolCommand

67. def usageText: String

    

    Definition Classes

    ToolCommand

68. def validateArgs(args: String*): Unit

    

    Definition Classes

    ToolCommand

69. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )