Packages

c

org.bdgenomics.adam.io

FastqRecordReader

abstract class FastqRecordReader extends RecordReader[Void, Text]

A record reader for the interleaved FASTQ format.

Reads over an input file and parses interleaved FASTQ read pairs into a single Text output. This is then fed into the FastqConverter, which converts the single Text instance into two Alignments.

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

Instance Constructors

  1. new FastqRecordReader(conf: Configuration, split: FileSplit)
    Attributes
    protected[io]

Abstract Value Members

  1. abstract def checkBuffer(bufferLength: Int, buffer: Text): Boolean

    Checks to see whether the buffer is positioned at a valid record.

    Checks to see whether the buffer is positioned at a valid record.

    bufferLength

    The length of the line currently in the buffer.

    buffer

    A buffer containing a peek at the first line in the current stream.

    returns

    Returns true if the buffer contains the first line of a properly formatted FASTQ record.

    Attributes
    protected[io]
  2. abstract def next(value: Text): Boolean

    Reads from the input split.

    Reads from the input split.

    value

    Text record to write input value into.

    returns

    Returns whether this read was successful or not.

    Attributes
    protected[io]
    See also

    #lowLevelFastqRead(Text, Text)

Concrete 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() @HotSpotIntrinsicCandidate()
  6. final def close(): Unit

    Close this RecordReader to future operations.

    Close this RecordReader to future operations.

    Definition Classes
    FastqRecordReader → RecordReader → Closeable → AutoCloseable
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  10. final def getCurrentKey(): Void

    FASTQ has no keys, so we return null.

    FASTQ has no keys, so we return null.

    returns

    Always returns null.

    Definition Classes
    FastqRecordReader → RecordReader
  11. final def getCurrentValue(): Text

    Returns the last interleaved FASTQ record.

    Returns the last interleaved FASTQ record.

    returns

    The text corresponding to the last read pair.

    Definition Classes
    FastqRecordReader → RecordReader
  12. final def getProgress(): Float

    How much of the input has the RecordReader consumed?

    How much of the input has the RecordReader consumed?

    returns

    Returns a value on [0.0, 1.0] that notes how many bytes we have read so far out of the total bytes to read.

    Definition Classes
    FastqRecordReader → RecordReader
  13. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  14. final def initialize(split: InputSplit, context: TaskAttemptContext): Unit
    Definition Classes
    FastqRecordReader → RecordReader
  15. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  16. final def lowLevelFastqRead(readName: Text, value: Text): Boolean

    Parses a read from an interleaved FASTQ file.

    Parses a read from an interleaved FASTQ file.

    Only reads a single record.

    readName

    Text record containing read name. Output parameter.

    value

    Text record containing full record. Output parameter.

    returns

    Returns true if read was successful (did not hit EOF).

    Attributes
    protected[io]
    Exceptions thrown

    RuntimeException Throws exception if FASTQ record doesn't have proper formatting (e.g., record doesn't start with @).

  17. final def makePositionMessage(): String

    Produces a debugging message with the file position.

    Produces a debugging message with the file position.

    returns

    Returns a string containing {filename}:{index}.

    Attributes
    protected[io]
  18. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  19. final def nextKeyValue(): Boolean

    Seeks ahead in our split to the next key-value pair.

    Seeks ahead in our split to the next key-value pair.

    Triggers the read of an interleaved FASTQ read pair, and populates internal state.

    returns

    True if reading the next read pair succeeded.

    Definition Classes
    FastqRecordReader → RecordReader
  20. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  21. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  22. final def positionAtFirstRecord(stream: FSDataInputStream, codec: CompressionCodec): Int

    Position the input stream at the start of the first record.

    Position the input stream at the start of the first record.

    stream

    The stream to reposition.

    Attributes
    protected[io]
  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. def toString(): String
    Definition Classes
    AnyRef → Any
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  27. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from RecordReader[Void, Text]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

Ungrouped