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