ADAM_2.12: Core 0.33.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package projections
  Definition Classes
    adam
- AlignmentField
- DbxrefField
- FeatureField
- FieldEnumeration
- FieldValue
- Filter
- FragmentField
- GenotypeField
- OntologyTermField
- Projection
- ReadField
- ReadGroupField
- ReferenceField
- SampleField
- SequenceField
- SliceField
- TranscriptEffectField
- VariantAnnotationField
- VariantCallingAnnotationsField
- VariantField

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org.bdgenomics.adam.projections

# AlignmentField 

###

#### object AlignmentField extends FieldEnumeration

Linear Supertypes
FieldEnumeration, Enumeration, Serializable, Serializable, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. AlignmentField
2. FieldEnumeration
3. Enumeration
4. Serializable
5. Serializable
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Type Members

1.  class Val extends Value with Serializable
   Attributes
     protected
   Definition Classes
     Enumeration
   Annotations
     @SerialVersionUID()
2.  abstract class Value extends Ordered[Value] with Serializable
   Definition Classes
     Enumeration
   Annotations
     @SerialVersionUID()
3.  class ValueSet extends AbstractSet[Value] with SortedSet[Value] with SortedSetLike[Value, ValueSet] with Serializable
   Definition Classes
     Enumeration
4.  class SchemaVal extends Val with FieldValue

   An enumerated field that is part of this schema.

   An enumerated field that is part of this schema.

   Definition Classes
     FieldEnumeration

### 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 SchemaValue: SchemaVal
   Attributes
     protected
   Definition Classes
     FieldEnumeration
5.  final def Value(i: Int, name: String): Value
   Attributes
     protected
   Definition Classes
     Enumeration
6.  final def Value(name: String): Value
   Attributes
     protected
   Definition Classes
     Enumeration
7.  final def Value(i: Int): Value
   Attributes
     protected
   Definition Classes
     Enumeration
8.  final def Value: Value
   Attributes
     protected
   Definition Classes
     Enumeration
9.  final def apply(x: Int): Value
   Definition Classes
     Enumeration
10.  final def asInstanceOf[T0]: T0
    Definition Classes
      Any
11.  val attributes: SchemaVal
12.  val basesTrimmedFromEnd: SchemaVal
13.  val basesTrimmedFromStart: SchemaVal
14.  val cigar: SchemaVal
15.  def clone(): AnyRef
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
16.  val duplicateRead: SchemaVal
17.  val end: SchemaVal
18.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
19.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
20.  val failedVendorQualityChecks: SchemaVal
21.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
22.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
23.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
24.  val insertSize: SchemaVal
25.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
26.  val mappingQuality: SchemaVal
27.  val mateAlignmentStart: SchemaVal
28.  val mateMapped: SchemaVal
29.  val mateNegativeStrand: SchemaVal
30.  val mateReferenceName: SchemaVal
31.  final def maxId: Int
    Definition Classes
      Enumeration
32.  val mismatchingPositions: SchemaVal
33.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
34.  var nextId: Int
    Attributes
      protected
    Definition Classes
      Enumeration
35.  var nextName: Iterator[String]
    Attributes
      protected
    Definition Classes
      Enumeration
36.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
37.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
38.  val originalCigar: SchemaVal
39.  val originalQualityScores: SchemaVal
40.  val originalStart: SchemaVal
41.  val primaryAlignment: SchemaVal
42.  val properPair: SchemaVal
43.  val qualityScores: SchemaVal
44.  val readGroupId: SchemaVal
45.  val readGroupSampleId: SchemaVal
46.  val readInFragment: SchemaVal
47.  val readMapped: SchemaVal
48.  val readName: SchemaVal
49.  val readNegativeStrand: SchemaVal
50.  val readPaired: SchemaVal
51.  def readResolve(): AnyRef
    Attributes
      protected
    Definition Classes
      Enumeration
52.  val recordSchema: Schema
    Definition Classes
      FieldEnumeration
53.  val referenceName: SchemaVal
54.  val secondaryAlignment: SchemaVal
55.  val sequence: SchemaVal
56.  val start: SchemaVal
57.  val supplementaryAlignment: SchemaVal
58.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
59.  def toString(): String
    Definition Classes
      Enumeration → AnyRef → Any
60.  def values: ValueSet
    Definition Classes
      Enumeration
61.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
62.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
63.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
64.  final def withName(s: String): Value
    Definition Classes
      Enumeration

### Inherited from FieldEnumeration

### Inherited from Enumeration

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped