org.bdgenomics.adam

# util

#### package util

Visibility

1. Public
2. All

### Type Members

1. #### case class DeletionEvent (readName: String, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

2. #### case class InsertionEvent (readName: String, insertedSequence: String, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

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

   Reads GATK-style interval list files e.

4. #### case class MatchEvent (readName: String, isReverseStrand: Boolean, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

5. #### class MdTag extends AnyRef

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

6. #### case class MismatchEvent (readName: String, mismatchedBase: Base.Value, isReverseStrand: Boolean, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

7. #### class ParquetFileTraversable [T <: IndexedRecord] extends Traversable[T]

8. #### class Pileup extends Serializable

9. #### abstract class PileupEvent extends Serializable

10. #### class PileupTraversable extends Traversable[Pileup] with Serializable

11. #### class QualityScore extends Ordered[QualityScore] with Serializable

12. #### class RegExp extends AnyRef

    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).

13. #### class TwoBitFile extends AnyRef

    Represents a set of reference sequences backed by a .

14. #### case class TwoBitRecord (dnaSize: Int, nBlocks: Seq[ReferenceRegion], maskBlocks: Seq[ReferenceRegion], dnaOffset: Int) extends Product with Serializable

### Value Members

1. #### object AttributeUtils

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

2. #### object Base extends Enumeration with Serializable

3. #### object HadoopUtil

4. #### object ImplicitJavaConversions

5. #### object MapTools

6. #### object MdTag

7. #### object MdTagEvent extends Enumeration

8. #### object NormalizationUtils

9. #### object ParquetLogger

10. #### object PhredUtils

11. #### object PileupTraversable extends Serializable

12. #### object QualityScore extends Serializable

13. #### object RegExp

14. #### object SequenceUtils

    This is a hack, and should be replaced! See Issue #410 -> https://github.

15. #### object TwoBitFile

16. #### object TwoBitRecord extends Serializable

17. #### object Util

18. #### object VcfHeaderUtils

    Convenience object for building a VCF header from sequence data.

19. #### object VcfStringUtils

### Ungrouped