Package

org.bdgenomics.adam

util

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package util

Visibility
  1. Public
  2. All

Type Members

  1. class IntervalListReader extends Traversable[(ReferenceRegion, String)]

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    Reads GATK-style interval list files e.g.

    Reads GATK-style interval list files e.g. example file taken from this page: http://www.broadinstitute.org/gatk/guide/article?id=1204

  2. class MdTag extends AnyRef

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    Represents the mismatches and deletions present in a read that has been aligned to a reference genome.

    Represents the mismatches and deletions present in a read that has been aligned to a reference genome. The MD tag can be used to reconstruct the reference that an aligned read overlaps.

  3. class ParquetFileTraversable[T <: IndexedRecord] extends Traversable[T]

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  4. class QualityScore extends Ordered[QualityScore] with Serializable

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  5. case class ReferenceContigMap(contigMap: Map[String, Seq[NucleotideContigFragment]]) extends ReferenceFile with Product with Serializable

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  6. trait ReferenceFile extends Serializable

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    File that contains a reference assembly that can be broadcasted

  7. class RegExp extends AnyRef

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    Wraps the java Pattern class, to allow for easier regular expression matching (including making the matches/finds methods return Option[Matcher], so that we can flatMap a set of strings with these methods).

  8. class TwoBitFile extends ReferenceFile

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    Represents a set of reference sequences backed by a .2bit file.

    Represents a set of reference sequences backed by a .2bit file.

    See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for the spec.

  9. class TwoBitFileSerializer extends Serializer[TwoBitFile]

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Value Members

  1. object AttributeUtils

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    AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.

  2. object Flattener

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  3. object ImplicitJavaConversions

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  4. object MapTools

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  5. object MdTag

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  6. object MdTagEvent extends Enumeration

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  7. object ParquetLogger

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  8. object PhredUtils

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  9. object QualityScore extends Serializable

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  10. object ReferenceContigMap extends Serializable

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  11. object RegExp

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  12. object TwoBitFile extends Serializable

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  13. object Util

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