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.
Sequence of bases in the read.
Reference sequence that the read is aligned to.
The CIGAR for the reference alignment.
The start position of the read alignment.
Returns a populated MD tag.
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.
Textual MD tag/mismatchingPositions string.
The read start position.
Cigar operators for the read
Returns a populated MD tag.
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 to write a new alignment for.
The Cigar for the new read alignment.
Reference sequence to write alignment against.
The position of the new read alignment.
Returns an MD tag for the new read alignment.
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.
apply
Given a single read and an updated Cigar, recalculates the MD tag.
Given a single read and an updated Cigar, recalculates the MD tag.
Record for current alignment.
Realigned cigar string.
Returns an MD tag for the new read alignment.
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.
apply
Companion object to MdTag case class. Provides methods for building an MdTag model from a read.