From an updated read alignment, writes a new MD tag.
From an updated read alignment, writes 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.
moveAlignment
From an updated read alignment, writes a new MD tag.
From an updated read alignment, writes a new MD tag.
Record for current alignment.
Realigned cigar string.
Returns an MD tag for the new read alignment.
moveAlignment
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