ADAM_2.12: Core 1.0.1 API < Back
 

# 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 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

t

org.bdgenomics.adam.ds.read

# AnySAMInFormatter 

###

#### trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[Alignment, Alignment, AlignmentDataset, T]

A trait that writes reads using an Htsjdk SAMFileWriter.

T

  The recursive type of the class that implements this trait.

Linear Supertypes
InFormatter[Alignment, Alignment, AlignmentDataset, T], Serializable, Serializable, AnyRef, Any
Known Subclasses
BAMInFormatter, SAMInFormatter
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. AnySAMInFormatter
2. InFormatter
3. Serializable
4. Serializable
5. AnyRef
6. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Abstract Value Members

1.  abstract val companion: InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]
   Attributes
     protected
   Definition Classes
     InFormatter
2.  abstract val converter: AlignmentConverter

   A converter from Alignment to SAMRecord.

3.  abstract val header: SAMFileHeader

   A serializable form of the SAM File Header.

4.  abstract def makeWriter(os: OutputStream): SAMFileWriter
   Attributes
     protected
5.  abstract val readGroups: ReadGroupDictionary

   A dictionary describing the read groups these reads are from.

### 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.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
6.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
8.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native() @HotSpotIntrinsicCandidate()
9.  def hashCode(): Int
   Definition Classes
     AnyRef → Any
   Annotations
     @native() @HotSpotIntrinsicCandidate()
10.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
11.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
12.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
13.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
14.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
15.  def toString(): String
    Definition Classes
      AnyRef → Any
16.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
17.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
18.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
19.  def write(os: OutputStream, iter: Iterator[Alignment]): Unit

    Writes alignments to an output stream in SAM format.

    Writes alignments to an output stream in SAM format.

    os

      An OutputStream connected to a process we are piping to.

    iter

      An iterator of records to write.

    Definition Classes
      AnySAMInFormatter → InFormatter

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated
   Deprecated

### Inherited from InFormatter[Alignment, Alignment, AlignmentDataset, T]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped