util

Type Members

1. class ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[K]

2. class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K]

3. trait ByteAccess extends AnyRef

   ByteAccess is a wrapper trait around sources of bytes which are accessible at arbitrary offsets.

4. class ByteArrayByteAccess extends ByteAccess with Serializable

5. class ByteArrayLocator extends FileLocator

6. 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.

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

8. trait FileLocator extends Serializable

   FileLocator is a trait which is meant to combine aspects of - Java's File - Hadoop's Path - S3 locations (including bucket and key) - classpath-relative URLs (classpath://, used in testing)

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

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

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

    Reads GATK-style interval list files e.

12. class LocalFileByteAccess extends ByteAccess

    This is somewhat poorly named, it probably should be LocalFileByteAccess

13. class LocalFileLocator extends FileLocator

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

15. class MdTag extends AnyRef

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

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

18. class Pileup extends Serializable

19. abstract class PileupEvent extends Serializable

20. class PileupTraversable extends Traversable[Pileup] with Serializable

21. class QualityScore extends Ordered[QualityScore] with Serializable

22. 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).

23. class S3ByteAccess extends ByteAccess

24. class S3FileLocator extends FileLocator

25. class SerializableAWSCredentials extends AWSCredentials with Serializable