util

Type Members

1. class CredentialsProperties extends Serializable with Logging

   CredentialsProperties is a wrapper class which extracts Amazon S3 keys (although it could be modified to extract other key / secret-key pairs) from a key-value-formatted file (see below), if available, or from the System environment otherwise.

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

3. class Histogram[T] extends Aggregated[T] with Serializable

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

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

   Reads GATK-style interval list files e.

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

7. class MdTag extends AnyRef

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

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

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

10. class Pileup extends Serializable

11. abstract class PileupEvent extends Serializable

12. class PileupTraversable extends Traversable[Pileup] with Serializable

13. class QualityScore extends Ordered[QualityScore] with Serializable

14. 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).

15. class SerializableAWSCredentials extends AWSCredentials with Serializable