org.bdgenomics.adam.io

BAMFilteredRecordReader

class BAMFilteredRecordReader extends BAMRecordReader

Scala implementation of BAMRecordReader, but with nextKeyValue() that filters by ReferenceRegion

Linear Supertypes
BAMRecordReader, RecordReader[LongWritable, SAMRecordWritable], Closeable, AutoCloseable, AnyRef, Any
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Inherited
  1. BAMFilteredRecordReader
  2. BAMRecordReader
  3. RecordReader
  4. Closeable
  5. AutoCloseable
  6. AnyRef
  7. Any
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Visibility
  1. Public
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Instance Constructors

  1. new BAMFilteredRecordReader()

Value Members

  1. final def !=(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. var bci: BlockCompressedInputStream

  6. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  7. def close(): Unit

    Definition Classes
    BAMFilteredRecordReader → BAMRecordReader → RecordReader → Closeable → AutoCloseable

  8. var codec: BAMRecordCodec

  9. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. var fileStart: Long

  12. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  13. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  14. def getCurrentKey(): LongWritable

    Definition Classes
    BAMFilteredRecordReader → BAMRecordReader → RecordReader

  15. def getCurrentValue(): SAMRecordWritable

    Definition Classes
    BAMFilteredRecordReader → BAMRecordReader → RecordReader

  16. def getProgress(): Float

    Definition Classes
    BAMRecordReader → RecordReader

  17. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  18. def initialize(spl: InputSplit, ctx: TaskAttemptContext): Unit

    Definition Classes
    BAMFilteredRecordReader → BAMRecordReader → RecordReader

  19. var isInitialized: Boolean

  20. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  21. val key: LongWritable

  22. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  23. final def nextKeyValue(): Boolean

    This method gets the nextKeyValue for our RecordReader, but filters by only returning records within a specified ReferenceRegion.

    This method gets the nextKeyValue for our RecordReader, but filters by only returning records within a specified ReferenceRegion. This function is tail recursive to avoid stack overflow when predicate data can be sparse.

    Definition Classes
    BAMFilteredRecordReader → BAMRecordReader → RecordReader
    Annotations
    @tailrec()

  24. final def notify(): Unit

    Definition Classes
    AnyRef

  25. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  26. val record: SAMRecordWritable

  27. var stringency: ValidationStringency

  28. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  29. def toString(): String

    Definition Classes
    AnyRef → Any

  30. var virtualEnd: Long

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  32. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  33. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from BAMRecordReader

Inherited from RecordReader[LongWritable, SAMRecordWritable]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

Ungrouped