digenicsearch

Type Members

1. case class AlleleCombination(a1: List[Short], a2: List[Short]) extends Product with Serializable

   

2. case class AnnotationFilter(key: String, method: (Double) ⇒ Boolean) extends Product with Serializable

   

3. case class AnnotationValue(key: String, value: List[Double]) extends Product with Serializable

   

4. case class Args(inputFiles: List[File] = Nil, outputDir: File = null, reference: File = null, regions: Option[File] = None, aggregation: Option[File] = None, pedFiles: List[File] = Nil, externalFiles: Map[String, File] = Map(), singleExternalFilters: List[AnnotationFilter] = Nil, pairExternalFilters: List[AnnotationFilter] = Nil, detectionMode: DetectionMode.Value = DetectionMode.Varant, singleAnnotationFilter: List[AnnotationFilter] = Nil, pairAnnotationFilter: List[AnnotationFilter] = Nil, fractions: FractionsCutoffs = FractionsCutoffs(), usingOtherFamilies: Boolean = false, maxDistance: Option[Long] = None, binSize: Int = 1000000, maxContigsInSingleJob: Int = 250, sparkMaster: Option[String] = None, onlyFamily: Option[String] = None) extends Product with Serializable

   

5. class ArgsParser extends AbstractOptParser[Args]

   

6. case class Broadcasts(samples: Array[String], dict: SAMSequenceDictionary, pedigree: PedigreeFileArray, annotations: Set[String], maxDistance: Option[Long], singleFilters: List[AnnotationFilter], pairFilters: List[AnnotationFilter], inputFiles: List[File], fractionsCutoffs: FractionsCutoffs, detectionMode: DetectionMode.Value, regions: Array[List[Region]], externalFiles: Array[File], externalFilesKeys: Array[String], singleExternalFilters: Array[List[ExternalFilter]], pairExternalFilters: Array[List[ExternalFilter]], usingOtherFamilies: Boolean) extends Product with Serializable

   

7. case class Combination(i1: Int, i2: Int) extends Product with Serializable

   

8. case class ExternalFilter(key: String, id: Int, method: (Double) ⇒ Boolean) extends Product with Serializable

   

9. case class Fraction(affected: Double, unaffected: Double) extends Product with Serializable

   

10. case class FractionsCutoffs(singleAffectedFraction: Double = 1.0, pairAffectedFraction: Double = 1.0, singleUnaffectedFraction: Double = 0, pairUnaffectedFraction: Double = 0, singleFamilyAffectedFraction: Double = 1.0, singleFamilyUnaffectedFraction: Double = 0) extends Product with Serializable

    

11. case class GeneCounts(gene: String, count: Long) extends Product with Serializable

    

12. case class GeneFamilyCounts(gene: String, count: Array[Long]) extends Product with Serializable

    

13. case class Genotype(alleles: List[Short]) extends Product with Serializable

    

14. case class GenotypeAnnotation(dp: Int, gq: Int) extends Product with Serializable

    

15. case class IndexedRegions(idx: Int, regions: List[Region]) extends Product with Serializable

    

16. class LoadRegion extends Iterator[Variant]

    

    This method will return a iterator of Variant

17. case class PedigreeFileArray(pedFile: PedigreeFile, samples: Array[String]) extends Product with Serializable

    

18. case class Region(contig: Int, start: Int, end: Int, name: String = "") extends Product with Serializable

    

19. case class ResultLineCsv(contig1: String, pos1: Int, contig2: String, pos2: Int, affectedFractions: String, familyAffectedFractions: String, externalFractions: String) extends Product with Serializable

    

20. case class Variant(contig: Int, pos: Int, alleles: List[String], genotypes: List[Genotype], annotations: List[AnnotationValue] = List(), genotypeAnnotation: List[GenotypeAnnotation], detectionResult: DetectionResult, externalGenotypes: Array[List[Genotype]], externalDetectionResult: Array[DetectionResult], regionsIdx: Int) extends Product with Serializable

    

    This stores a variant and genotypes in a compressed format

21. case class VariantCombination(v1: Variant, v2: Variant, alleles: List[AlleleCombination]) extends Product with Serializable

    

22. case class VariantCsv(contig: String, pos: Int, alleles: String, pedigreeFractions: String, externalFractions: String) extends Product with Serializable