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.
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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]
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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.
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- protected[io]
- See also
#lowLevelFastqRead(Text, Text)
Concrete Value Members
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final
def
!=(arg0: Any): Boolean
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clone(): AnyRef
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def
close(): Unit
Close this RecordReader to future operations.
Close this RecordReader to future operations.
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- FastqRecordReader → RecordReader → Closeable → AutoCloseable
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final
def
eq(arg0: AnyRef): Boolean
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equals(arg0: Any): Boolean
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finalize(): Unit
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def
getClass(): Class[_]
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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
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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
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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.
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- FastqRecordReader → RecordReader
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def
hashCode(): Int
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final
def
initialize(split: InputSplit, context: TaskAttemptContext): Unit
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- FastqRecordReader → RecordReader
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final
def
isInstanceOf[T0]: Boolean
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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).
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- protected[io]
- Exceptions thrown
RuntimeException
Throws exception if FASTQ record doesn't have proper formatting (e.g., record doesn't start with @).
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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}.
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final
def
ne(arg0: AnyRef): Boolean
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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.
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- FastqRecordReader → RecordReader
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def
notify(): Unit
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def
notifyAll(): Unit
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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.
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synchronized[T0](arg0: ⇒ T0): T0
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