org.bdgenomics.adam.rdd

# variation

#### package variation

Visibility

1. Public
2. All

### Type Members

1. #### class ADAMVCFOutputFormat [K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

2. #### class ConcordanceTable extends AnyRef

   Helper class for maintaining the genotype concordance table and computing the relevant metrics.

3. #### class GenotypeRDDFunctions extends Serializable with Logging

4. #### case class GenotypesSummary (perSampleStatistics: StatisticsMap, singletonCount: Long, distinctVariantCount: Long) extends Product with Serializable

   Summary statistics for a set of genotypes.

5. #### case class GenotypesSummaryCounts (genotypesCounts: GenotypeAlleleCounts, singleNucleotideVariantCounts: VariantCounts, multipleNucleotideVariantCount: Long, insertionCount: Long, deletionCount: Long, readCount: Option[Long], phasedCount: Long) extends Product with Serializable

   Simple counts of various properties across a set of genotypes.

6. #### class VariantContextRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[VariantContext] with Logging

### Value Members

1. #### object ADAMVCFOutputFormat extends Serializable

2. #### object ConcordanceTable

3. #### object GenotypesSummary extends Serializable

4. #### object GenotypesSummaryCounts extends Serializable

5. #### object GenotypesSummaryFormatting

   Functions for converting a GenotypesSummary object to various text formats.

### Ungrouped