Packages

c

org.bdgenomics.adam.io

InterleavedFastqInputFormat

final class InterleavedFastqInputFormat extends FastqInputFormat

This class is a Hadoop reader for "interleaved fastq" -- that is, fastq with paired reads in the same file, interleaved, rather than in two separate files. This makes it much easier to Hadoopily slice up a single file and feed the slices into an aligner. The format is the same as fastq, but records are expected to alternate between /1 and /2. As a precondition, we assume that the interleaved FASTQ files are always uncompressed; if the files are compressed, they cannot be split, and thus there is no reason to use the interleaved format.

This reader is based on the FastqInputFormat that's part of Hadoop-BAM, found at https://github.com/HadoopGenomics/Hadoop-BAM/blob/master/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java

Linear Supertypes
FastqInputFormat, FileInputFormat[Void, Text], InputFormat[Void, Text], AnyRef, Any
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Inherited
  1. InterleavedFastqInputFormat
  2. FastqInputFormat
  3. FileInputFormat
  4. InputFormat
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new InterleavedFastqInputFormat()

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. def addInputPathRecursively(arg0: List[FileStatus], arg1: FileSystem, arg2: Path, arg3: PathFilter): Unit
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. def computeSplitSize(arg0: Long, arg1: Long, arg2: Long): Long
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  8. def createRecordReader(genericSplit: InputSplit, context: TaskAttemptContext): RecordReader[Void, Text]

    Creates the new record reader that underlies this input format.

    Creates the new record reader that underlies this input format.

    genericSplit

    The split that the record reader should read.

    context

    The Hadoop task context.

    returns

    Returns the interleaved FASTQ record reader.

    Definition Classes
    InterleavedFastqInputFormat → InputFormat
  9. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  10. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. def getBlockIndex(arg0: Array[BlockLocation], arg1: Long): Int
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  12. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  13. def getFormatMinSplitSize(): Long
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  14. def getSplits(arg0: JobContext): List[InputSplit]
    Definition Classes
    FileInputFormat → InputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  15. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  16. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  17. def isSplitable(context: JobContext, filename: Path): Boolean

    Checks to see if the file we are looking at is splittable.

    Checks to see if the file we are looking at is splittable.

    A file is splittable if it is:

    - Uncompressed. - Compressed with the BGZFEnhancedGzipCodec _and_ the underlying stream is a BGZF stream. BGZFEnhancedGzipCodec looks for files with a .gz extension, which means that the codec may be selected if the file is a non-block GZIPed file, and thus is non-splittable. To validate this, we use HTSJDKs in-built mechanism for checking if a stream is a BGZF stream. - Any other splittable codec (e.g., .bgz/BGZFCodec, .bz2/BZip2Codec)

    context

    The job context to get the configuration from.

    filename

    The path the input file is saved at.

    returns

    Returns false if this file is compressed.

    Attributes
    protected[io]
    Definition Classes
    FastqInputFormat → FileInputFormat
  18. def listStatus(arg0: JobContext): List[FileStatus]
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  19. def makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String], arg4: Array[String]): FileSplit
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  20. def makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String]): FileSplit
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  21. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  22. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  23. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  24. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  25. def toString(): String
    Definition Classes
    AnyRef → Any
  26. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  28. 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 FastqInputFormat

Inherited from FileInputFormat[Void, Text]

Inherited from InputFormat[Void, Text]

Inherited from AnyRef

Inherited from Any

Ungrouped