util

Type Members

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

   

   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

   

   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]

   

4. class QualityScore extends Ordered[QualityScore] with Serializable

   

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

   

6. trait ReferenceFile extends Serializable

   

   File that contains a reference assembly that can be broadcasted

7. 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).

8. class TwoBitFile extends ReferenceFile

   

   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]