org.bdgenomics.adam.util

# MdTag

#### object MdTag

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1. #### final def !=(arg0: Any): Boolean

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2. #### final def ##(): Int

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3. #### final def ==(arg0: Any): Boolean

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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(read: RichAlignmentRecord, newCigar: Cigar, newReference: String, newAlignmentStart: Long): MdTag

   From an updated read alignment, writes a new MD tag.

   From an updated read alignment, writes 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.

   See also

     moveAlignment

6. #### def apply(read: RichAlignmentRecord, newCigar: Cigar): MdTag

   From an updated read alignment, writes a new MD tag.

   From an updated read alignment, writes a new MD tag.

   read

     Record for current alignment.

   newCigar

     Realigned cigar string.

   returns

     Returns an MD tag for the new read alignment.

   See also

     moveAlignment

7. #### def apply(mdTagInput: String, referenceStart: Long): 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.

   returns

     Returns a populated MD tag.

8. #### final def asInstanceOf[T0]: T0

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9. #### def clone(): AnyRef

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16. #### def moveAlignment(read: RichAlignmentRecord, 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

17. #### def moveAlignment(read: RichAlignmentRecord, 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

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