Packages

c

com.jnpersson.discount.fastdoop

FASTQReadsRecordReader

class FASTQReadsRecordReader extends RecordReader[Text, QRecord]

This class reads <key, value> pairs from an InputSplit. The input file is in FASTQ format. A FASTA record has a header line that is the key, the data line, an optional single line header string and a quality line.

Example: @SRR034939.184 090406_HWI-EAS68_9096_FC400PR_PE_1_1_10 length=100 CCACCTCCTGGGTTCAAGGGGTTCTCTTGCCTCAGCTNNNNNNNNNNNNGGNNNNNNNNNTNNNN +SRR034939.184 090406_HWI-EAS68_9096_FC400PR_PE_1_1_10 length=100 HDHFHHHHHHFFAFF6?<:<HHHHHHHHHEDHHHF##!!!!!!!!!!!!##!!!!!!!!!#!!!! ...

Version

1.0

See also

InputSplit

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

Instance Constructors

  1. new FASTQReadsRecordReader()

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
    FASTQReadsRecordReader → RecordReader → Closeable → AutoCloseable
    Annotations
    @Override()
  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
    FASTQReadsRecordReader → RecordReader
    Annotations
    @Override()
  12. def getCurrentValue(): QRecord
    Definition Classes
    FASTQReadsRecordReader → RecordReader
    Annotations
    @Override()
  13. def getProgress(): Float
    Definition Classes
    FASTQReadsRecordReader → RecordReader
    Annotations
    @Override()
  14. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  15. def initialize(genericSplit: InputSplit, context: TaskAttemptContext): Unit
    Definition Classes
    FASTQReadsRecordReader → RecordReader
    Annotations
    @Override()
  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
    FASTQReadsRecordReader → RecordReader
    Annotations
    @Override()
  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, QRecord]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

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