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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### 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