package read
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Type Members
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class
ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
- K
The key type. Keys are not written.
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class
ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
- K
The key type. Keys are not written.
-
class
ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
- K
The key type. Keys are not written.
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class
ADAMCRAMOutputFormatHeaderLess[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
- K
The key type. Keys are not written.
- class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
- class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
- sealed abstract class AlignmentDataset extends AvroReadGroupGenomicDataset[Alignment, Alignment, AlignmentDataset]
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trait
AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[Alignment, Alignment, AlignmentDataset, T]
A trait that writes reads using an Htsjdk SAMFileWriter.
A trait that writes reads using an Htsjdk SAMFileWriter.
- T
The recursive type of the class that implements this trait.
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trait
AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]
Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
- T
The type of the underlying InFormatter.
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case class
AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[Alignment] with Product with Serializable
An OutFormatter that automatically infers whether the piped input is SAM or BAM.
An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.
- case class BAMInFormatter extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable
- case class DatasetBoundAlignmentDataset extends AlignmentDataset with DatasetBoundGenomicDataset[Alignment, Alignment, AlignmentDataset] with Product with Serializable
- case class DatasetBoundReadDataset extends ReadDataset with DatasetBoundGenomicDataset[Read, Read, ReadDataset] with Product with Serializable
- class FASTQInFormatter extends InFormatter[Alignment, Alignment, AlignmentDataset, FASTQInFormatter]
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case class
IncorrectMDTagException(read: Alignment, mdTag: String) extends Exception with Product with Serializable
A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
- read
The read whose MD tag was recomputed, with original MD tag.
- mdTag
The recomputed MD tag.
- case class ParquetUnboundAlignmentDataset extends AlignmentDataset with Product with Serializable
- case class ParquetUnboundReadDataset extends ReadDataset with Product with Serializable
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case class
QualityScoreBin(low: Int, high: Int, score: Int) extends Product with Serializable
A bin to put quality scores in.
A bin to put quality scores in.
- low
The lowest quality score in the bin.
- high
The highest quality score in the bin.
- score
The score to assign to all these bases.
- case class RDDBoundAlignmentDataset extends AlignmentDataset with Product with Serializable
- case class RDDBoundReadDataset extends ReadDataset with Product with Serializable
- sealed abstract class ReadDataset extends AvroGenomicDataset[Read, Read, ReadDataset]
- class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]
- case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable
- class SingleReadBucketSerializer extends Serializer[SingleReadBucket]
Value Members
- object AlignmentDataset extends Serializable
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object
BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable
InFormatter companion for building an InFormatter that streams BAM.
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object
FASTQInFormatter extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, FASTQInFormatter] with Serializable
InFormatter companion that creates an InFormatter that writes FASTQ.
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object
QualityScoreBin extends Serializable
Companion object for creating quality score bins.
- object ReadDataset
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object
SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable
InFormatter companion for building an InFormatter that streams SAM.