Package

org.bdgenomics.adam.rdd

read

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package read

Visibility
  1. Public
  2. All

Type Members

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

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  2. class ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

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  3. class ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

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  4. class ADAMCRAMOutputFormatHeaderLess[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

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

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  6. class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

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  7. case class AlignedReadRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Product with Serializable

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  8. sealed trait AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD]

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  9. trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[AlignmentRecord, AlignmentRecordRDD, T]

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  10. trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, T]

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  11. class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

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  12. case class BAMInFormatter(header: SAMFileHeaderWritable, recordGroups: RecordGroupDictionary, converter: AlignmentRecordConverter) extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable

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

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  14. 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

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

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

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  17. class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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  18. class InstrumentedADAMCRAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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  19. class InstrumentedADAMCRAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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

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  21. class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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

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  23. case class SAMInFormatter(header: SAMFileHeaderWritable, recordGroups: RecordGroupDictionary, converter: AlignmentRecordConverter) extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

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  24. case class UnalignedReadRDD(rdd: RDD[AlignmentRecord], recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Unaligned with Product with Serializable

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Value Members

  1. object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable

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  2. object DuplicateMetrics extends Serializable

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  3. object FlagStat

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  4. object FlagStatMetrics extends Serializable

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  5. object MDTagging extends Serializable

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  6. object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

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  7. object UnalignedReadRDD extends Serializable

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  8. package realignment

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  9. package recalibration

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