Packages

c

com.jnpersson.discount.fastdoop

IndexedFastaReader

class IndexedFastaReader extends RecordReader[Text, PartialSequence]

FASTA file reader that uses a faidx (.fai) file to track sequence locations. .fai indexes can be generated by various tools, for example seqkit: https://github.com/shenwei356/seqkit/

This reader can read a mix of full and partial sequences. If the sequence is fully contained in this split, it will be read as a single PartialSequence record. Otherwise, it will be read as multiple records. Partial sequences can be identified and reassembled using their header (corresponding to sequence ID) and seqPosition fields.

Partial sequences are read together with (k-1) bps from the next part to ensure that full k-mers can be processed.

The reader for every split must stream the FAI file. Thus, it is not recommended to use this reader for e.g. short reads, or when the maximum size of a sequence is relatively small. ShortReadsRecordReader and FASTQReadsRecordReader are better suited to such a task. For reading a single long sequence without a FAI index, LongReadsRecordReader can be used instead.

Version

1.0

See also

IndexedFastaFormat

Linear Supertypes
RecordReader[Text, PartialSequence], Closeable, AutoCloseable, AnyRef, Any
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Inherited
  1. IndexedFastaReader
  2. RecordReader
  3. Closeable
  4. AutoCloseable
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new IndexedFastaReader()

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. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  6. def close(): Unit
    Definition Classes
    IndexedFastaReader → RecordReader → Closeable → AutoCloseable
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. def getCurrentKey(): Text
    Definition Classes
    IndexedFastaReader → RecordReader
  12. def getCurrentValue(): PartialSequence
    Definition Classes
    IndexedFastaReader → RecordReader
  13. def getProgress(): Float
    Definition Classes
    IndexedFastaReader → RecordReader
  14. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  15. def initialize(genericSplit: InputSplit, context: TaskAttemptContext): Unit
    Definition Classes
    IndexedFastaReader → RecordReader
  16. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  17. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  18. def nextKeyValue(): Boolean
    Definition Classes
    IndexedFastaReader → RecordReader
  19. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  20. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  21. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  22. def toString(): String
    Definition Classes
    AnyRef → Any
  23. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  24. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from RecordReader[Text, PartialSequence]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

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