ADAM_2.12: Core 1.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package ds
  Definition Classes
    adam
-  package feature
  Definition Classes
    ds
-  package fragment
  Definition Classes
    ds
-  package read
  Definition Classes
    ds
- ADAMBAMOutputFormat
- ADAMBAMOutputFormatHeaderLess
- ADAMCRAMOutputFormat
- ADAMCRAMOutputFormatHeaderLess
- ADAMSAMOutputFormat
- ADAMSAMOutputFormatHeaderLess
- AlignmentDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentDataset
- DatasetBoundReadDataset
- FASTQInFormatter
- IncorrectMDTagException
- ParquetUnboundAlignmentDataset
- ParquetUnboundReadDataset
- QualityScoreBin
- RDDBoundAlignmentDataset
- RDDBoundReadDataset
- ReadDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer
-  package sequence
  Definition Classes
    ds
-  package variant
  Definition Classes
    ds

p

org.bdgenomics.adam.ds

# read 

#### package read

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Ordering

1. Alphabetic

Visibility

1. Public
2. All

### Type Members

1.  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.

2.  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.

3.  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.

4.  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.

5.  class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
6.  class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
7.  sealed abstract class AlignmentDataset extends AvroReadGroupGenomicDataset[Alignment, Alignment, AlignmentDataset]
8.  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.

9.  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.

10.  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.

11.  case class BAMInFormatter extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable
12.  case class DatasetBoundAlignmentDataset extends AlignmentDataset with DatasetBoundGenomicDataset[Alignment, Alignment, AlignmentDataset] with Product with Serializable
13.  case class DatasetBoundReadDataset extends ReadDataset with DatasetBoundGenomicDataset[Read, Read, ReadDataset] with Product with Serializable
14.  class FASTQInFormatter extends InFormatter[Alignment, Alignment, AlignmentDataset, FASTQInFormatter]
15.  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.

16.  case class ParquetUnboundAlignmentDataset extends AlignmentDataset with Product with Serializable
17.  case class ParquetUnboundReadDataset extends ReadDataset with Product with Serializable
18.  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.

19.  case class RDDBoundAlignmentDataset extends AlignmentDataset with Product with Serializable
20.  case class RDDBoundReadDataset extends ReadDataset with Product with Serializable
21.  sealed abstract class ReadDataset extends AvroGenomicDataset[Read, Read, ReadDataset] with MultisampleGenomicDataset[Read, Read, ReadDataset]
22.  class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]
23.  case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable
24.  class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

### Value Members

1.  object AlignmentDataset extends Serializable
2.  object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable

   InFormatter companion for building an InFormatter that streams BAM.

3.  object FASTQInFormatter extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, FASTQInFormatter] with Serializable

   InFormatter companion that creates an InFormatter that writes FASTQ.

4.  object QualityScoreBin extends Serializable

   Companion object for creating quality score bins.

5.  object ReadDataset
6.  object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

   InFormatter companion for building an InFormatter that streams SAM.

### Ungrouped