PrefilterReads

Value Members

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

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

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3. final def ##(): Int

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

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

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6. def apply(rdd: AlignmentRecordRDD, args: PrefilterReadsArgs): AlignmentRecordRDD

   Filters out reads and contigs that should not be processed.

   Filters out reads and contigs that should not be processed.

   rdd

   RDD of reads and associated metadata.

   args

   Arguments specifying the filters to apply.

   returns

   Returns a new AlignmentRecordRDD where reads that we don't want to use in genotyping have been discarded, and where contigs that we don't want to genotype have been removed.

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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9. def contigFilterFn(args: PrefilterReadsArgs): (String) ⇒ Boolean

   args

   The arguments specifying which contigs to keep.

   returns

   Returns a function that returns true if a contig with a given name should be kept.

   Attributes

   protected[org.bdgenomics.avocado.util]

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

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11. def equals(arg0: Any): Boolean

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12. def filterGrcAutosome(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the naming scheme for GRCh autosomal chromosomes.

    Attributes

    protected[org.bdgenomics.avocado.util]

13. def filterGrcMitochondrial(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the GRCh mitochondrial chromosome name.

    Attributes

    protected[org.bdgenomics.avocado.util]

14. def filterGrcSex(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the naming scheme for GRCh sex chromosomes.

    Attributes

    protected[org.bdgenomics.avocado.util]

15. def filterMapped(read: AlignmentRecord, keepNonPrimary: Boolean): Boolean

    read

    Read to test for filtration.

    returns

    Returns true if the read is aligned.

    Attributes

    protected[org.bdgenomics.avocado.util]

16. def filterMappingQuality(read: AlignmentRecord, minMappingQuality: Int): Boolean

    read

    Read to test for filtration.

    minMappingQuality

    Only keep reads with a mapping quality above this value.

    returns

    Returns true if the read is aligned.

    Attributes

    protected[org.bdgenomics.avocado.util]

17. def filterNonGrcAutosome(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the naming scheme for HG/UCSC autosomal chromosomes.

    Attributes

    protected[org.bdgenomics.avocado.util]

18. def filterNonGrcMitochondrial(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the HG/UCSC mitochondrial chromosome name.

    Attributes

    protected[org.bdgenomics.avocado.util]

19. def filterNonGrcSex(contigName: String): Boolean

    contigName

    Contig name to test for filtration.

    returns

    Returns true if the contig matches the naming scheme for HG/UCSC sex chromosomes.

    Attributes

    protected[org.bdgenomics.avocado.util]

20. def filterUnique(read: AlignmentRecord): Boolean

    read

    Read to test for filtration.

    returns

    Returns true if the read is not a duplicate read.

    Attributes

    protected[org.bdgenomics.avocado.util]

21. def finalize(): Unit

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

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23. def hashCode(): Int

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24. final def isInstanceOf[T0]: Boolean

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

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26. final def notify(): Unit

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27. final def notifyAll(): Unit

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28. def readFilterFn(args: PrefilterReadsArgs, contigFilterFn: (String) ⇒ Boolean): (AlignmentRecord) ⇒ Boolean

    args

    The arguments specifying which reads to keep.

    contigFilterFn

    A function that determines which contigs should be kept, given the contig name.

    returns

    Returns a function that returns true if a read should be kept.

    Attributes

    protected[org.bdgenomics.avocado.util]

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

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30. def toString(): String

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31. final def wait(): Unit

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

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

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