org.bdgenomics.adam

# util

#### package util

Visibility

1. Public
2. All

### 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]

### 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 Flattener

3. #### object ImplicitJavaConversions

4. #### object MapTools

5. #### object MdTag

6. #### object MdTagEvent extends Enumeration

7. #### object NormalizationUtils

8. #### object ParquetLogger

9. #### object PhredUtils

10. #### object QualityScore extends Serializable

11. #### object ReferenceContigMap extends Serializable

12. #### object RegExp

13. #### object TwoBitFile extends Serializable

14. #### object Util

15. #### object VcfHeaderUtils

    Convenience object for building a VCF header from sequence data.

### Ungrouped