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
- Alphabetic
- By Inheritance
- InterleavedFastqInputFormat
- FastqInputFormat
- FileInputFormat
- InputFormat
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
- new InterleavedFastqInputFormat()
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
addInputPathRecursively(arg0: List[FileStatus], arg1: FileSystem, arg2: Path, arg3: PathFilter): Unit
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
- Annotations
- @throws( classOf[java.io.IOException] )
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
def
computeSplitSize(arg0: Long, arg1: Long, arg2: Long): Long
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
-
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
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
getBlockIndex(arg0: Array[BlockLocation], arg1: Long): Int
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
getFormatMinSplitSize(): Long
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
-
def
getSplits(arg0: JobContext): List[InputSplit]
- Definition Classes
- FileInputFormat → InputFormat
- Annotations
- @throws( classOf[java.io.IOException] )
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
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
-
def
listStatus(arg0: JobContext): List[FileStatus]
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
- Annotations
- @throws( classOf[java.io.IOException] )
-
def
makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String], arg4: Array[String]): FileSplit
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
-
def
makeSplit(arg0: Path, arg1: Long, arg2: Long, arg3: Array[String]): FileSplit
- Attributes
- protected[input]
- Definition Classes
- FileInputFormat
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
Deprecated Value Members
-
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.