ADAM_2.12: Core 0.29.0 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 rdd
  Definition Classes
    adam
-  package read
  Definition Classes
    rdd
- ADAMBAMOutputFormat
- ADAMBAMOutputFormatHeaderLess
- ADAMCRAMOutputFormat
- ADAMCRAMOutputFormatHeaderLess
- ADAMSAMOutputFormat
- ADAMSAMOutputFormatHeaderLess
- AlignmentRecordDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentRecordDataset
- DatasetBoundReadDataset
- FASTQInFormatter
- IncorrectMDTagException
- InstrumentedADAMBAMOutputFormat
- InstrumentedADAMBAMOutputFormatHeaderLess
- InstrumentedADAMCRAMOutputFormat
- InstrumentedADAMCRAMOutputFormatHeaderLess
- InstrumentedADAMSAMOutputFormat
- InstrumentedADAMSAMOutputFormatHeaderLess
- ParquetUnboundAlignmentRecordDataset
- ParquetUnboundReadDataset
- QualityScoreBin
- RDDBoundAlignmentRecordDataset
- RDDBoundReadDataset
- ReadDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer

c

org.bdgenomics.adam.rdd.read

# IncorrectMDTagException 

###

#### case class IncorrectMDTagException(read: AlignmentRecord, 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.

read

  The read whose MD tag was recomputed, with original MD tag.

mdTag

  The recomputed MD tag.

Linear Supertypes
Serializable, Product, Equals, Exception, Throwable, Serializable, AnyRef, Any
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Ordering

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2. By Inheritance

Inherited

1. IncorrectMDTagException
2. Serializable
3. Product
4. Equals
5. Exception
6. Throwable
7. Serializable
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new IncorrectMDTagException(read: AlignmentRecord, mdTag: String)

   read

     The read whose MD tag was recomputed, with original MD tag.

   mdTag

     The recomputed MD tag.

### 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 addSuppressed(arg0: Throwable): Unit
   Definition Classes
     Throwable
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  def clone(): AnyRef
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
7.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
8.  def fillInStackTrace(): Throwable
   Definition Classes
     Throwable
9.  def finalize(): Unit
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
10.  def getCause(): Throwable
    Definition Classes
      Throwable
11.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  def getLocalizedMessage(): String
    Definition Classes
      Throwable
13.  def getMessage(): String
    Definition Classes
      IncorrectMDTagException → Throwable
14.  def getStackTrace(): Array[StackTraceElement]
    Definition Classes
      Throwable
15.  final def getSuppressed(): Array[Throwable]
    Definition Classes
      Throwable
16.  def initCause(arg0: Throwable): Throwable
    Definition Classes
      Throwable
17.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
18.  val mdTag: String
19.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
20.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
21.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
22.  def printStackTrace(arg0: PrintWriter): Unit
    Definition Classes
      Throwable
23.  def printStackTrace(arg0: PrintStream): Unit
    Definition Classes
      Throwable
24.  def printStackTrace(): Unit
    Definition Classes
      Throwable
25.  val read: AlignmentRecord
26.  def setStackTrace(arg0: Array[StackTraceElement]): Unit
    Definition Classes
      Throwable
27.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
28.  def toString(): String
    Definition Classes
      Throwable → AnyRef → Any
29.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
30.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
31.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from Exception

### Inherited from Throwable

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped