org.bdgenomics.adam

# util

#### package util

Visibility

1. Public
2. All

### Type Members

1. #### case class IndexedFastaFile (sc: SparkContext, filePath: String, stringency: ValidationStringency = ...) extends ReferenceFile with Logging with Product with Serializable

   Loads and extracts sequences directly from indexed fasta or fa files.

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

   Implements a traversable collection that is backed by a Parquet file.

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

   A broadcastable ReferenceFile backed by a map containing contig name -> Seq[NucleotideContigFragment] pairs.

4. #### class ReferenceContigMapSerializer extends Serializer[ReferenceContigMap]

5. #### trait ReferenceFile extends Serializable

   File that contains a reference assembly that can be broadcasted

6. #### class TwoBitFile extends ReferenceFile

   Represents a set of reference sequences backed by a .

7. #### 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 GenomeFileReader

   Object for reading Bedtools genome files from disk.

3. #### object ParquetLogger

   Helper object for setting the logging level for Parquet.

4. #### object PhredUtils extends Serializable

   Helper singleton for converting Phred scores to/from probabilities.

5. #### object ReferenceContigMap extends Serializable

   Companion object for creating a ReferenceContigMap from an RDD of contig fragments.

6. #### object SequenceDictionaryReader

   Object for reading sequence dictionary files (.

7. #### object TextRddWriter

   Writes an RDD to disk as text and optionally merges.

### Ungrouped