Packages

c

org.bdgenomics.adam.io

FastqInputFormat

abstract class FastqInputFormat extends FileInputFormat[Void, Text]

Licensed to Big Data Genomics (BDG) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The BDG licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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

Instance Constructors

  1. new FastqInputFormat()

Abstract Value Members

  1. abstract def createRecordReader(arg0: InputSplit, arg1: TaskAttemptContext): RecordReader[Void, Text]
    Definition Classes
    InputFormat
    Annotations
    @throws( classOf[java.io.IOException] ) @throws( ... )

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. 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. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  10. def getBlockIndex(arg0: Array[BlockLocation], arg1: Long): Int
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  11. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  12. def getFormatMinSplitSize(): Long
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  13. def getSplits(arg0: JobContext): List[InputSplit]
    Definition Classes
    FileInputFormat → InputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  14. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  15. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  16. 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
  17. def listStatus(arg0: JobContext): List[FileStatus]
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  18. def makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String], arg4: Array[String]): FileSplit
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  19. def makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String]): FileSplit
    Attributes
    protected[input]
    Definition Classes
    FileInputFormat
  20. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  21. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  22. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  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 FileInputFormat[Void, Text]

Inherited from InputFormat[Void, Text]

Inherited from AnyRef

Inherited from Any

Ungrouped