ADAM_2.12: Core 0.35.0 API < Back
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-  package adam
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o

org.bdgenomics.adam.models

# MdTag 

###
Companion class MdTag

#### object MdTag extends Serializable

Companion object to MdTag case class. Provides methods for building an MdTag model from a read.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
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### Value Members

1.  final def !=(arg0: Any): Boolean
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     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
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4.  def apply(read: String, reference: String, cigar: Cigar, start: Long): MdTag

   Creates an MD tag object given a read, and the accompanying reference alignment.

   Creates an MD tag object given a read, and the accompanying reference alignment.

   read

     Sequence of bases in the read.

   reference

     Reference sequence that the read is aligned to.

   cigar

     The CIGAR for the reference alignment.

   start

     The start position of the read alignment.

   returns

     Returns a populated MD tag.

5.  def apply(mdTagInput: String, referenceStart: Long, cigar: Cigar): MdTag

   Builds an MD tag object from the string representation of an MD tag and the start position of the read.

   Builds an MD tag object from the string representation of an MD tag and the start position of the read.

   mdTagInput

     Textual MD tag/mismatchingPositions string.

   referenceStart

     The read start position.

   cigar

     Cigar operators for the read

   returns

     Returns a populated MD tag.

6.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
7.  def clone(): AnyRef
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     protected[lang]
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     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
8.  final def eq(arg0: AnyRef): Boolean
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9.  def equals(arg0: Any): Boolean
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10.  final def getClass(): Class[_]
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      @native() @HotSpotIntrinsicCandidate()
11.  def hashCode(): Int
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12.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
13.  def moveAlignment(read: RichAlignment, newCigar: Cigar, newReference: String, newAlignmentStart: Long): MdTag

    Given a single read, an updated reference, and an updated Cigar, this method calculates a new MD tag.

    Given a single read, an updated reference, and an updated Cigar, this method calculates a new MD tag.

    read

      Read to write a new alignment for.

    newCigar

      The Cigar for the new read alignment.

    newReference

      Reference sequence to write alignment against.

    newAlignmentStart

      The position of the new read alignment.

    returns

      Returns an MD tag for the new read alignment.

    Note

      If the alignment start position has not changed (e.g., the alignment change is that an indel in the read was left normalized), then the two argument (RichADAMRecord, Cigar) moveAlignment function should be used.

    See also

      apply

14.  def moveAlignment(read: RichAlignment, newCigar: Cigar): MdTag

    Given a single read and an updated Cigar, recalculates the MD tag.

    Given a single read and an updated Cigar, recalculates the MD tag.

    read

      Record for current alignment.

    newCigar

      Realigned cigar string.

    returns

      Returns an MD tag for the new read alignment.

    Note

      For this method, the read must be mapped and adjustments to the cigar must not have led to a change in the alignment start position. If the alignment position has been changed, then the moveAlignment function with a new reference must be used.

    See also

      apply

15.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
16.  final def notify(): Unit
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      AnyRef
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      @native() @HotSpotIntrinsicCandidate()
17.  final def notifyAll(): Unit
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      @native() @HotSpotIntrinsicCandidate()
18.  final def synchronized[T0](arg0: ⇒ T0): T0
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19.  def toString(): String
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20.  final def wait(arg0: Long, arg1: Int): Unit
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      @throws( ... )
21.  final def wait(arg0: Long): Unit
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22.  final def wait(): Unit
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### Deprecated Value Members

1.  def finalize(): Unit
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     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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