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Type Members

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

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

3. class AlignmentRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord]

4. case class DuplicateMetrics(total: Long, bothMapped: Long, onlyReadMapped: Long, crossChromosome: Long) extends Product with Serializable

5. case class FlagStatMetrics(total: Long, duplicatesPrimary: DuplicateMetrics, duplicatesSecondary: DuplicateMetrics, mapped: Long, pairedInSequencing: Long, read1: Long, read2: Long, properlyPaired: Long, withSelfAndMateMapped: Long, singleton: Long, withMateMappedToDiffChromosome: Long, withMateMappedToDiffChromosomeMapQ5: Long, failedQuality: Boolean) extends Product with Serializable

6. case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception with Product with Serializable

7. class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

8. class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

9. case class MDTagging(reads: RDD[AlignmentRecord], referenceFile: ReferenceFile, partitionSize: Long = 1000000, overwriteExistingTags: Boolean = false, validationStringency: ValidationStringency = ...) extends Logging with Product with Serializable